Primary Citation PubMed: 8875929
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
Data mentions are occurrences of PDB IDs in the full text articles from the
PubMedCentral Open Access Subset
of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed.
Article titles can be filtered by keywords and sorted by year.
Targeting MDM2 by the small molecule RITA: towards the development of new multi-target drugs against cancer.
(2005) Theor Biol Med Model 2
PubMed: 16174299 | PubMedCentral: PMC1243243 | DOI: 10.1186/1742-4682-2-38
Materials and methods Protein preparation The X-ray structure of human MDM2 in complex with the p53 transactivation domain was used in the present study (PDB code: 1YCR ).
Publication Year: 2005
The unfoldomics decade: an update on intrinsically disordered proteins.
(2008) BMC Genomics 9 Suppl 2
PubMed: 18831774 | PubMedCentral: PMC2559873 | DOI: 10.1186/1471-2164-9-S2-S1
A ribbon diagram of complex of MDM2 (green) and P53 fragment (red) was regenerated from PDB 1YCR .
Publication Year: 2008
Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling.
(2009) PLoS Comput Biol 5
PubMed: 19165315 | PubMedCentral: PMC2613531 | DOI: 10.1371/journal.pcbi.1000267
Structures: allophycocyanin 1all:B (A), phosphotransferase 1apm:E (B), human CDC42 gene regulation protein 1grn:AB (C), oncogene protein 1ycr (D), signal transduction protein 1shc (E), large fragment ... f Thermus aquaticus DNA polymerase I 2ktq (with the DNA chain in yellow) (F).
Publication Year: 2009
Unfoldomics of human diseases: linking protein intrinsic disorder with diseases.
(2009) BMC Genomics 10 Suppl 1
PubMed: 19594884 | PubMedCentral: PMC2709268 | DOI: 10.1186/1471-2164-10-S1-S7
The Protein Data Bank IDs and partner names for the structures (from upper left, clockwise) are as follows: ( 1tsr DNA), ( 1gzh 53BP1), ( 1q2d gcn5), ( 3sak p53 (tet dom)), ( 1xqh set9), ( 1h26 cyclin... ), ( 1ma3 sirtuin), ( 1jsp CBP bromo domain), ( 1dt7 s100bb), ( 2h1l sv40 Large T antigen), ( 1ycs 53BP2), ( 2gs0 PH), ( 1ycr MDM2), and ( 2b3g rpa70).
Peptide, Peptidomimetic, and Small-molecule Antagonists of the p53-HDM2 Protein-Protein Interaction.
(2006) Int J Pept Res Ther 12
PubMed: 19617922 | PubMedCentral: PMC2710987 | DOI: 10.1007/s10989-006-9016-5
A likely conformation of terphenyl 5b (light sticks) was modelled and aligned with the three p53 residue side chains (PDB # 1YCR).
The modelled binding mode of 8d [based on NMR studies (Stoll et al., 2001 )] into the structure of the p53–HDM2 complex (PDB # 1YCR) is shown on the right.
Constructed from PDB # 1YCR.
Constructed from PDB # 1YCR & 1Z1M.
, 2005 ), of compound 16c (solid sticks) in the p53 peptide (F19, W23, L26 side chains shown as thin sticks) binding pocket of HDM2 (surface, from PDB # 1YCR) is shown on the right.
The Phe, 6-Cl-Trp, and Leu residues of the peptidomimetic are depicted as sticks, the remainder as a secondary structure cartoon only; the corresponding p53 peptide residue side chains (alignment with PDB # 1YCR) are shown as light sticks, and the HDM2 surface is depicted as a mesh.
The HDM2-bound (PDB # 1YCR) relative conformations of the p53 residues F19, W23, and L26 are shown.
Publication Year: 2006
Human cancer protein-protein interaction network: a structural perspective.
PubMed: 20011507 | PubMedCentral: PMC2785480 | DOI: 10.1371/journal.pcbi.1000601
The interaction is represented by a known complex structure in PDB  as 1ycr.
Modulation of p53 binding to MDM2: computational studies reveal important roles of Tyr100.
(2009) BMC Bioinformatics 10 Suppl 15
PubMed: 19958516 | PubMedCentral: PMC2788357 | DOI: 10.1186/1471-2105-10-S15-S6
Methods The 'open' state of MDM2 (residues 25-109) was obtained from the crystal structure of the MDM2-p53 complex (RCSB entry 1YCR , resolved at 2.6 Å) [ 10 ].
Figure 1 MDM2 in surface representation, taken from various structures available in PDB, complexed with various ligands including WT p53 ( 1YCR ), a β-hairpin peptide ( 2AXI ), small molecule 'nutlin' ( 1RV1 ), an 8-mer p53 peptide analogue ( 2GV2 ), an optimized peptide ( 1T4F ) and a 12 residue peptide .
We have used molecular dynamics simulations to examine three different conformations of MDM2: (i) 'Open' state of the conformation taken from the wild type (WT) complex ( 1YCR ) with the Y100 side chain pointing away from the binding pocket; (ii) 'closed' state - the conformation of MDM2 taken from the complex with α-helical P27S mutant of p53 with the Y100 side chain pointing towards the binding pocket; (iii) The 'apo' state - the unliganded state of MDM2, obtained from the ensemble of NMR structures [ 8 ] where Y100 is in a deeply buried position (see Figure 2 ).
Both, the crystal structure (PDB code 1YCR ) [ 10 ] and molecular dynamics (MD) simulations of the complex of MDM2 and a 13 residue fragment of the transactivation domain of p53 show that Y100 points away from the binding pocket and forms a hydrogen bond (HB) with either the backbones of E28 or N29 of wild type (WT) p53 peptide.
If the p53 peptide is extended at its C-terminus (as seen in the crystal structure 1YCR ), the side chain hydroxyl of Y100 is involved in hydrogen bond (HB) with the backbone of either E28 or N29 of the p53 peptide; however the p53 peptide can also adopt an α-helical conformation at its C-terminus and this is potentiated by the Y100 hydroxyl forming an HB with the backbone of L26 which provides a 'cozier' fit between the p53 peptide and MDM2 [ 7 ].
Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database.
(2010) PLoS One 5
PubMed: 20231898 | PubMedCentral: PMC2834754 | DOI: 10.1371/journal.pone.0009598
Class # Family Complex a Number of Inhibitors b Source c Affinity d (nM) Ref I 1 BclX L /Bak 1bxl 8 PubMed 340  I 2 MDM2/p53 1ycr 1ycq 3 PubMed 600  I 3 XIAP BI... 3/CASPASE 9 1nw9 2 PubMed 20  I 4 XIAP BIR3/SMAC 1g73 5 PubMed 420  I 5 ZipA/FtsZ 1f47 4 PubMed 20,000  II 6 Chagasin/Papain 3e1z 1 PDB 0.036 e  II 7 E2/E1 1tue 1 PubMed na  II 8 FKBP12/TGFR 1b6c 17 PDB na  II 9 IL-2/IL-2R 1z92 8 PubMed 10  II 10 MMP1/TIMP1 2j0t 1 PDB 0.40 e  II 11 MMP3/TIMP1 1oo9 1 PDB 0.22 e  II 12 Subtilisin/Eglin C 1cse 1r0r 1to2 1 PDB 0.029  –  II 13 Thrombin/Protein C inhibitor 3b9f 1 PDB na  II 14 Trypsin/Trypsin inhibitor 2uuy 3 PDB 0.02  PPIs were subdivided into class I that correspond to protein/peptide interactions with less than six segments at the interface (families 1–5) and class II that represent more globular interacting domains with more segments (families 6–14).
Publication Year: 2010
Binding-site assessment by virtual fragment screening.
PubMed: 20404926 | PubMedCentral: PMC2852417 | DOI: 10.1371/journal.pone.0010109
d For Bcl-xl and MDM2, we used two structures, peptide-bound (1bxl and 1ycr, respectively) and small ligand bound (1ysn and 1rv1, respectively).
ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery.
(2010) Nucleic Acids Res 38
PubMed: 20525787 | PubMedCentral: PMC2896143 | DOI: 10.1093/nar/gkq502
Visualization tool showing anchor residues Phe19, Trp23 and Leu26 of p53 from PDB 1YCR (PPI: p53-MDM2).
Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example.
(2009) Mol Biosyst 5
PubMed: 19585003 | PubMedCentral: PMC2898629 | DOI: 10.1039/B905661K
Fig. 7A illustrates the interaction between Mdm2 and the transactivation domain of p53 (PDB code: 1ycr; 1ycrAB is the PRISM labeled interface).
Oligobenzamide proteomimetic inhibitors of the p53-hDM2 protein-protein interaction.
(2009) Chem Commun (Camb)
PubMed: 20448956 | PubMedCentral: PMC2898631 | DOI: 10.1039/b908207g
34 Fig. 1 (a) Crystal structure of h DM2 in complex with a p53 peptide (PDB ID: 1YCR) and (b) the p53 peptide showing side chains key for binding.
Anchoring intrinsically disordered proteins to multiple targets: lessons from N-terminus of the p53 protein.
(2011) Int J Mol Sci 12
PubMed: 21541066 | PubMedCentral: PMC3083713 | DOI: 10.3390/ijms12021410
Initial conformations for MD simulations were taken from the p53N-MDM2 complex (PDB ID 1YCR) [ 62 ] (trajectories MS1–MS10), the p53N-Taz2 complex (PDB ID 2K8F) [ 88 ] (trajectories TS1ȁ... ;TS5), or the disordered state of unbound p53N (trajectories DS1–DS5).
Publication Year: 2011
Swimming into peptidomimetic chemical space using pepMMsMIMIC.
(2011) Nucleic Acids Res 39
PubMed: 21622954 | PubMedCentral: PMC3125738 | DOI: 10.1093/nar/gkr287
Interestingly, starting from the crystallographic structure of MDM2/p53 complex reported in our demo key-study (PDB code: 1YCR), all five nutlin analogues were ranked among the top 0.6% of the entire ... ulticonfMMsINC® database using the combined ShS and PFS filtering.
C-terminal substitution of MDM2 interacting peptides modulates binding affinity by distinctive mechanisms.
(2011) PLoS One 6
PubMed: 21904608 | PubMedCentral: PMC3164098 | DOI: 10.1371/journal.pone.0024122
The crystal structure (1YCR) of the complex between p53 and MDM2 does not contain the coordinates of the residue Q16.
Computer simulations The crystal structure (PDB code 1YCR) of the complex between MDM2 (residues 25–109) and a p53 peptide (residues 17–29) was used as a template to model the complexes studied  .
The template for modeling of all complexes was the crystal structure of MDM2-p53 (PDB code 1YCR; (  )), where residues 19–25 of the p53 peptide form an α-helix, and the other residues are unstructured.
Molecular basis of Bcl-X(L)-p53 interaction: insights from molecular dynamics simulations.
PubMed: 22039431 | PubMedCentral: PMC3198449 | DOI: 10.1371/journal.pone.0026014
The wild type human p53 (residues 17–29) and MDM2 (residues 25–109) complex crystal structure with PDB ID: 1YCR was utilized  .
Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists.
(2012) PLoS One 7
PubMed: 22427896 | PubMedCentral: PMC3299697 | DOI: 10.1371/journal.pone.0032839
(b) In the p53/MDM2 complex (PDB 1YCR) three residues (F19, W23, L25) of p53 (green sticks) are buried in MDM2 (yellow surface).
In both structures the indole anchor analog of tryptophan overlaps almost perfectly with W23 in p53 (shown in yellow sticks), when the receptors are aligned the MDM2 structure in the co-crystal (PDB 1YCR).
The results of AnchorQuery pharmacophore search are first quickly minimized within a fixed receptor (PDB 1YCR) with no solvent model and Coulomb electrostatics to eliminate ligand poses that are sterically or electrostatically infeasible.
Publication Year: 2012
Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets.
(2012) BMC Bioinformatics 13
PubMed: 22417279 | PubMedCentral: PMC3359218 | DOI: 10.1186/1471-2105-13-39
Table 4 Structures used in protein-ligand and protein-protein pocket analysis Target protein (PDB id of apo structure) Inhibitor (PDB id) Protein partner (PDB id) Bcl-X L ) acyl sulfonamide derivative... Bak (1LXL) (1YSI) (1BXL) MDM2 benzodiazapine derivative p53 (1Z1M) (1T4E) (1YCR) Xiap apoptosis inhibitor naphthalenamide derivative Caspase 9 Bir3 domain (1F9X) (1TFQ) (1NW9) Xiap apoptosis inhibitor Smac peptidomimetic SMAC caspase activator Bir3 domain (1F9X) (2JK7) (1G73) ZipA indoloquinolizin inhibitor 1 FtsZ (1F46) (1S1J) (1F47) HPV11 E2 protein tetrahydrofuran derivative HPV11 E1 protein (1RK6) (1R6N) (1TUE) (1R6N) Interleukin 2 diphenyl derivative IL2-Receptor (1M47) (1M48) (1Z92) HIV-1 Integrase chlorophenyl-dihydroquinolin acetic acid LEDGF (3L3U) (3LPT) (2B4J) TNFa subunit A chromen-4-one derivative TNFa subunit B (1TNF) (2AZ5) (1TNF) TNF receptor 1a thiazolidin-4-one derivative TNF-beta (1EXT) (1FT4) (1TNR) MDM4 subunit A chlorobenzyl-phenyl-imidazol derivative p53 (3DAB) (3LBJ) (3DAB) Structures used in comparative analyses (detailed in Tables 1 and 2) are taken from the 2P2I database of protein-protein complexes with known inhibitors of the protein-protein interaction.
Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules.
(2012) J Chem Theory Comput 8
PubMed: 22798729 | PubMedCentral: PMC3392909 | DOI: 10.1021/ct300117j
(A) The MDM2 structure 35 (1YCR) in ribbon representation and interaction spots from probe mixture simulation 1–5 ( Table S2 ) as spheres are shown.
Simulating molecular mechanisms of the MDM2-mediated regulatory interactions: a conformational selection model of the MDM2 lid dynamics.
PubMed: 22815859 | PubMedCentral: PMC3397965 | DOI: 10.1371/journal.pone.0040897
Structural changes in the MDM2 receptor (residue 26–109) upon binding of the phosphorylated lid in the two lowest energy clusters ( B, D ) were compared with the MDM2 receptor in the complex w... th p53 (PDB ID 1YCR ) (shown in magenta).
All publically available crystal structures of the MDM2 protein from PDB were used to categorize the conformational space of MDM2, including the crystal structure of xenopus MDM2 bound to the transactivation domain of p53(PDB ID 1YCQ)  ; the crystal structure of human MDM2 bound to the transactivation domain of p53(PDB ID 1YCR)  ; the crystal structure of human MDM2 with an imidazole inhibitor nutlin (PDB ID 1RV1)  ; the crystal structure of human MDM2 in complex with a beta-hairpin PDB ID 2AXI)  ; the crystal structure of the MDM2 complex with an 8-mer p53 peptide analogue (PDB ID 2GV2)  ; the crystal structures of human MDM2 in the complex with a p53-derived peptide (PDB ID 1T4F) and a benzodiazepine inhibitor (PDB ID 1T4E)  ; an ensemble of 24 NMR structures of apo-MDM2 (PDB ID 1Z1M)  ; and the NMR structure of a complex between MDM2 and a small molecule inhibitor (PDB ID 1TTV)  .
To study the effect of lid binding on the p53-MDM2 interactions, we have used the co-crystal structure of the p53-MDM2 complex (PDB ID 1YCR)  as the initial conformation of the N-terminal MDM2 domain, and attached the lid residues from the crystal structure of MDM2 with the benzodiazepine inhibitor (PDB ID 1T4E)  to the N-terminus after structural alignment of the two structures.
The “|closed” form of the bound pS17 lid compared with p53 binding (PDB ID 1YCR).
( A ) The contact map of the p53 residues with the HDM2 receptor in the crystal structure of the p53-MDM2 complex (PDB ID 1YCR).
Structural changes in the MDM2 receptor (residue 26–109) upon binding of the phosphorylated lid in the two lowest energy clusters ( B, D ) were compared with the MDM2 receptor in the complex with p53 (PDB ID 1YCR ) (shown in magenta).
The “|closed” form of the bound S17D lid compared with p53 binding (PDB ID 1YCR).
Binding of Translationally Controlled Tumour Protein to the N-terminal domain of HDM2 is inhibited by nutlin-3.
PubMed: 22912717 | PubMedCentral: PMC3418249 | DOI: 10.1371/journal.pone.0042642
Model was constructed by docking the structures of the two proteins (for HDM2, the N-terminal domain consisting of residues 25–109, RCSB entry 1YCR  ; for TCTP, residues 1–172, RCS... entry 1YZ1).
Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable.
PubMed: 22916232 | PubMedCentral: PMC3423354 | DOI: 10.1371/journal.pone.0043253
Figures were generated using the matchmaker function from Chimera to superpose hDM2 from PDB code 1T4F to pdb codes: a) 1YCR; b) 1RV1; c) 1T4E.
Molecular dynamic simulation insights into the normal state and restoration of p53 function.
(2012) Int J Mol Sci 13
PubMed: 22949826 | PubMedCentral: PMC3431824 | DOI: 10.3390/ijms13089709
The three-dimensional structures of p53 TAD fragment bound to MDM2 (PDB ID: 1YCR, Figure 1A ) [ 18 ] and p53 CTD fragment bound to S100 calcium-binding protein B (PDB 1DT7, Figure 1D ) [ 19 ] are show... in Figure 1 .
For example, the TAD fragment of p53 involving residues 12–26, has high probability of forming a short α-helix that is capable of interacting with protein partners, such as the transformed mouse 3T3 cell double minute 2 (MDM2, or HDM2 for the human congener, PDB ID: 1YCR, Figure 1A ) [ 18 ] and MDM2-related protein (MDMX, also named MDM4) [ 27 ].
The complex of p53-MDM2 (PDB 1YCR) [ 18 ] is shown in cartoon, p53 TAD fragment (residues 17–29) is shown in yellow and the three most important residues Phe19, Trp23 and Leu26 are shown in stick, MDM2 (residues 25–109) is shown in white and the four residues Leu54, His96, Ile99 and Tyr100 in MDM2 are shown in green and stick; The complex of p53-MDMX (PDB 3DAB) [ 27 ] is shown in cartoon, p53 TAD fragment (residues 17–29) is shown in orange and the three most important residues Phe19, Trp23 and Leu26 are shown in stick, MDMX (residues 23–110) is shown in grey and the equivalent residues Met53, Pro95, Leu98 and Tyr99 in MDMX are shown in light magenta and stick; the spatial orientation of the side chains of Phe19 and Trp23 of p53 are highly similar, but that of Leu26 is different in p53-MDM2 and p53-MDMX complex.
( A ) The complex of p53 transcriptional activation domain (TAD) fragment bound to MDM2 (PDB 1YCR) [ 18 ] is shown in cartoon, p53 TAD fragment (residues 17–29) is shown in magenta and the three most important residues are shown in stick, MDM2 (residues 25–109) is shown in green; ( B ) The tetramer of the DBD of p53 (PDB 3KMD) [ 15 ] is shown in cartoon and the four monomers (residues 92–291) are colored in green, cyan, magenta and yellow, respectively; Zn 2+ is shown in sphere and dirtyviolet, and the DNA is shown in stick; ( C ) The tetramer of oligomerization domain (OD) of p53 (PDB 1PES) [ 16 ] is shown in cartoon and the four monomers (residues 325–355) are colored in green, cyan, magenta and yellow, respectively; ( D ) The complex of p53 C-terminal regulatory domain (CTD) fragment bound to S100 calcium-binding protein B (PDB 1DT7) [ 19 ] is shown in cartoon, p53 CTD fragment (residues 377–387) is shown in magenta and yellow, S100B (residues 1–91) is shown in green and cyan and the two Ca 2+ are shown in sphere and are colored in, consistent with the S100B protein for the two subunits, respectively.
The three-dimensional structure of p53-MDM2 (PDB ID: 1YCR) ( Figures 1A and 3 ) [ 18 ] reveals that the peptide segment (Glu17-Asn29) of p53 TAD as an amphipathic α-helix binds to the deep hydrophobic cleft, which is formed by the N-terminal domain of MDM2 (Glu25-Val109) containing of two pairs of α-helices and an anti-parallel β-sheets.
Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1? and PKR.
(2012) BMC Struct Biol 12
PubMed: 23148689 | PubMedCentral: PMC3534215 | DOI: 10.1186/1472-6807-12-28
Modeling of p53 transactivation domain [PDB id: 1YCR] bound to ck1α showed the analogy of substrate recognition and interaction with ck1α.
COEUS: "semantic web in a box" for biomedical applications.
(2012) J Biomed Semantics 3
PubMed: 23244467 | PubMedCentral: PMC3554586 | DOI: 10.1186/2041-1480-3-11
From UniProt data we also extract PharmGKB (PA30196, PA26282…) and PDB (2PCX, 1YCR…) identifiers, among others.
Evaluation of Hydration Free Energy by Level-Set Variational Implicit-Solvent Model with Coulomb-Field Approximation.
(2013) J Chem Theory Comput 9
PubMed: 23505345 | PubMedCentral: PMC3596957 | DOI: 10.1021/ct301087w
Note that d = 0 Å corresponds to their native configuration in the crystal structures (PDB code: 1YCR ).
The wild type p53/MDM2 (PDB code 1YCR ) complex involves a hydrophobic binding pocket.
Publication Year: 2013
In vitro selection of mutant HDM2 resistant to Nutlin inhibition.
(2013) PLoS One 8
PubMed: 23653682 | PubMedCentral: PMC3641235 | DOI: 10.1371/journal.pone.0062564
The N terminus of HDM2 was extended from residue 25 (as in 1YCR) by grafting residues 19–24 from 4ERF  (resolved at 2.0 Å) on to 1YCR.
Molecular Dynamics Simulations Interactions between the N terminal domain of HDM2 and the N terminal domain of p53 or Nutlin: To model the interactions of the N terminal domain of HDM2 with p53 and Nutlin, the crystal structures of the HDM2-p53 complex  (PDB code 1YCR, resolved at 2.6 Å) and the HDM2-Nutlin complex  (PDB code 1RV1, resolved at 2.3 Å) were used.
Functional diversity and structural disorder in the human ubiquitination pathway.
PubMed: 23734257 | PubMedCentral: PMC3667038 | DOI: 10.1371/journal.pone.0065443
C ) Interaction between E3 ligase MDM2 and P53 (P53 tumor suppressor protein, also TP53; PDB 1YCR), here the substrate undergoes induced folding upon binding to the folded SWIB domain of MDM2.
Computational analysis of protein-protein interfaces involving an alpha helix: insights for terphenyl-like molecules binding.
(2013) BMC Pharmacol Toxicol 14
PubMed: 23768251 | PubMedCentral: PMC3689098 | DOI: 10.1186/2050-6511-14-31
( c ) Structure of human E3 ubiquitin-protein ligase MDM2 (code entry 1YCR) binding domain.
( f ) human E3 ubiquitin-protein ligase MDM2 and p53 tumor transactivation domain, code entry 1YCR.
Figure 4 Illustration of the interacting residues (in sticks) of the protein (atom color type) and the bound peptide (red): ( a ) chicken calmodulin and smMLCK (code entry 2O5G), ( b ) human centrin 2 and the centrin binding region of XPC (code entry 2GGM), ( c ) human BCL-XL protein and BAK (code entry 1BXL), ( d ) human E3 ubiquitin- protein ligase MDM2 and p53 tumor transactivation domain (code entry 1YCR), ( e ) rabbit cardiac troponin C and cardiac troponin I (code entry 1A2X).
Table 1 Protein – alpha-helical peptide complexes Protein complex PDB code Resolution SwissProt code Interacting residues of the bound alpha-helix Chicken calmodulin in complex with smooth muscle myosin light chain kinase (smMLCK) 2O5G * P62149 TRP5, THR8, VAL12 1.08 Å Human calmodulin in complex with a mutant peptide of human DRP-1 kinase 1ZUZ P62158 TRP305, PHE309, VAL312 1.91 Å Human calmodulin in complex with CAV1.1 IQ peptide 2VAY * P62158 THR526, ILE529, PHE533 1.94 Å Human calmodulin in complex with CAV2.2 IQ peptide 3DVE P62158 MET854, VAL857, MET161 2.35 Å E Coli calmodulin in complex with RS20 peptide of smMLCK 1QTX - TRP5, THR8, VAL12 1.65 Å Rat calmodulin in complex with NMDA receptor NR1C1peptide 2HQW P62161 PHE880, THR884, LEU887 1.90 Å Human centrin 2 in complex with the centrin binding region of XPC protein 2GGM P41208 TRP848, LEU851, LEU855 2.35 Å C-terminal domain of human centrin 2 in complex with a repeat sequence of human Sfi 1 2K2I P41208 LEU651, LEU655, TRP658 NMR Scherffelia dubia centrin in complex with smMLCK peptide 3KF9 Q06827 TRP4, PHE8, VAL11 2.60 Å Human BCL-XL in complex with BAK peptide 1BXL * Q07817 VAL574, LEU578, ILE581 NMR Human E3 ubiquitin-protein ligase MDM2 in complex with p53 tumor transactivation domain (fragment 17-125) 1YCR * Q00987 PHE19, TRP23, LEU26 2.60 Å Rabbit cardiac troponin C in complex with a fragment (residues 1-47) of cardiac troponin I 1A2X P02586 LEU17, MET21, ILE24 2.30 Å *known to be disrupted by terphenyl or its derivatives.
( a ) Human E3 ubiquitin-protein ligase MDM2 (PDB code 1YCR), ( b ) Scherffelia dubia centrin (PDB code 3KF9).
Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.
PubMed: 23869206 | PubMedCentral: PMC3712014 | DOI: 10.1371/journal.pone.0067051
A high resolution crystal structure of the MDM2-p53 protein interaction is available in the PDB (pdbid: 1YCR)  and was used to create a starting structure ( figure 9A ).
A) Crystal structure of p53 (pink sticks) - MDM2 (electrostatic surface) protein interaction with three hotspot residues highlighted (Phe19, Trp23, Leu26) which are responsible for majority of interaction's binding affinity (pdbid: 1YCR).
Effect of sequence and stereochemistry reversal on p53 peptide mimicry.
PubMed: 23922660 | PubMedCentral: PMC3726663 | DOI: 10.1371/journal.pone.0068723
From the crystal structure of p53/MDM2 (PDB code: 1YCR  , resolution 2.6 Å), the distances between Phe 19 and Trp 23 and between Trp 23 and Leu 26 are in a narrow range of 5.7–6.2 ... #x000c5; over both α- and β-carbon measures ( Table 3 ).
The d 1 , d 2 and d 3 values from crystallographic structure of N-terminal sequence of p53 bound to MDM2 also given (PDB 1YCR  ).
Solid-phase methodology for synthesis of O-alkylated aromatic oligoamide inhibitors of ?-helix-mediated protein-protein interactions.
(2013) Chemistry 19
PubMed: 23508712 | PubMedCentral: PMC3743211 | DOI: 10.1002/chem.201204098
Figure 1 a) α-Helix (taken from protein database ID: 1YCR) with i , i +4 and i +7 side chains highlighted; b) chemical structure of 3- O -alkylated oligoamide helix mimetic c) energy minimised... structure of a helix mimetic with R 3 =R 2 =R 3 = i Pr; d) idealized α-helix superimposed onto minimised aromatic oligoamide.
On the intrinsic disorder status of the major players in programmed cell death pathways.
(2013) F1000Res 2
PubMed: 24358900 | PubMedCentral: PMC3829196 | DOI: 10.12688/f1000research.2-190.v1
Residues 17–125 of MDM2 (blue surface) in a complex with the transactivation domain of p53 (residues 15–29, red ribbon) (PDB ID: 1YCR); G .
Inhibition of nutlin-resistant HDM2 mutants by stapled peptides.
PubMed: 24278380 | PubMedCentral: PMC3835680 | DOI: 10.1371/journal.pone.0081068
For this, residues 19-24 of HDM2 were crafted from 4ERF resolved at 2.0Å [ 39 ] on to 1YCR, so as the initial structure includes residues 19 -109 of HDM2.
In order to examine the dynamics of the full N-terminal region of HDM2 we grafted 11 conformations of the lid (residues 1-24) from the ensemble of NMR structures (1Z1M)[ 37 ] onto 1YCR (residues 25-109).
In addition, there is a recent crystal structure of HDM2 (residues 6-109) that has become available (in complex with a small molecule; PDB code 4HBM, resolved at 1.9Å)[ 38 ] with an ordered lid and so we also created a 12 th structure of 1YCR where we grafted this lid (only from residues 6-24).
Heterogeneous Hydration of p53/MDM2 Complex.
(2014) J Chem Theory Comput 10
PubMed: 24803860 | PubMedCentral: PMC3958133 | DOI: 10.1021/ct400967m
Figure 1 p53/MDM2 complex (PDB code: 1ycr.
Theory and Methods A System Preparation The initial structure of the p53/MDM2 complex is taken from the Protein Data Bank (PDB code: 1ycr.
Publication Year: 2014
HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors.
(2014) J Chem Inf Model 54
PubMed: 24521147 | PubMedCentral: PMC3966529 | DOI: 10.1021/ci4005332
Table 1 K i and K d Binding Affinity Data Set of Protein–Protein Interaction Inhibitors a interaction biological role PDB (complex) K d (complex) (M) Bcl-x L /Bak programme... cell death 1bxl 3.4 × 10 –7 modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 1 N3B 4369509 Bcl-x L 1ysi 1.2 × 10 –7 2 ABT-737 11228183 Bcl-x L 2yxj 5.0 × 10 –10 3 4FC 2782689 Bcl-x L 1ysg 3.0 × 10 –5 4 TN1 68258 Bcl-x L 1ysg 4.3 × 10 –3 5 LIU 15991562 Bcl-2 2o22 6.7 × 10 –8 6 W1191542 44182311 Bcl-x L 3inq 1.1 × 10 –8 interaction biological role PDB (complex) K d (complex) (M) MDM2/p53 transcription regulation 1ycr 6.0 × 10 –7 modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 7 HDM2 656933 MDM2 1t4e 8.0 × 10 –8 8 WK23 44825260 MDM2 3lbk 9.2 × 10 –7 9 MI-63 72200152 MDM2 3lbl 3.6 × 10 –8 interaction biological role PDB (complex) K d (complex) (M) XIAP-BIR3/CASPASE-9 programmed cell death 1nw9 2.0 × 10 –8 modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 10 998 4369343 XIAP-BIR3 1tfq 1.2 × 10 –8 11 997 5388929 XIAP-BIR3 1tft 5.0 × 10 –9 12 9JZ 72199974 XIAP-BIR3 3hl5 3.4 × 10 –5 interaction biological role PDB (complex) K d (complex) (M) XIAP-BIR3/SMAC programmed cell death 1g73 4.2 × 10 –7 modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥K d (modulator) (M) 13 BI6 72199334 XIAP-BIR3 2jk7 6.7 × 10 –8 14 AoxSPW 24916924 XIAP-BIR3 2opy 3.0 × 10 –5 15 Smac005 25011737 XIAP-BIR3 3clx 1.2 × 10 –7 16 Smac005 25011737 XIAP-BIR3 3cm7 1.2 × 10 –7 17 Smac010 25011738 XIAP-BIR3 3cm2 4.2 × 10 –7 18 Smac037 25058143 XIAP-BIR3 3eyl 2.2 × 10 –7 19 CZ3 72199333 XIAP-BIR3 3g76 2.3 × 10 –7 interaction biological role PDB (complex) K d (complex) (M) ZipA/FtsZ cell cycle regulation/cellular structure 1f47 2.0 × 10 –5 modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 20 WAI 656967 ZipA 1y2f 1.2 × 10 –5 21 CL3 5287936 ZipA 1y2g 8.3 × 10 –5 interaction biological role PDB (complex) K d (complex) (M) HPV-E2/E1 viral infection 1tue n/d modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 22 BILH 434 5287508 HPV-E2 1r6n 4.0 × 10 –8 interaction biological role PDB (complex) K d (complex) (M) IL-2/IL-2R immune system regulation 1z92 1.0 × 10 –8 modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 23 FRG 5288250 IL-2 1m48 2.2 × 10 –5 24 FRB 23586028 IL-2 1pw6 7.0 × 10 –6 25 SP-1985 5287951 IL-2 1m49 7.5 × 10 –6 26 FRH 5288251 IL-2 1py2 1.0 × 10 –7 27 SP-4160 656989 IL-2 1qvn 1.4 × 10 –6 a Original references for the affinity data are provided in the Supporting Information (Table S1).
Table 2 IC50 Binding Affinity Data Set of Protein–Protein Interaction Inhibitors a interaction biological role PDB (complex) K d (complex) (M) Bcl-x L /Bak programmed cell death 1bxl 3.4 × 10 –7 modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) IC50 (modulator) (M) 28 HI0 24798804 Bcl-x L 3qkd 3.0 × 10 –09 29 0Q5 56973540 Bcl-x L 4ehr 1.3 × 10 –08 interaction biological role PDB (complex) K d (complex) (M) LEDGF/75-integrase programmed cell death 2b4j 1.1 × 10 –8 modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) IC50 (modulator) (M) 30 723 921795 75-integrase 3lpt 1.2 × 10 –5 31 976 45281242 75-integrase 3lpu 1.4 × 10 –6 32 TQ2 44199170 75-integrase 4e1m 2.2 × 10 –7 33 TQX 44198672 75-integrase 4e1n 1.9 × 10 –8 interaction biological role PDB (complex) K d (complex) (M) MDM2/p53 transcription regulation 1ycr 6 × 10 –7 modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) IC50 (modulator) (M) 34 IMY 49867154 MDM2 1ttv 1.6 × 10 –7 35 YIN 5594130 MDM2 3jzk 1.2 × 10 –6 36 0R2 56591324 MDM2 4ere 4.2 × 10 –9 37 0R3 56965957 MDM2 4erf 1.1 × 10 –9 38 BLF 56951871 MDM2 4dij 3.0 × 10 –8 interaction biological role PDB (complex) K d (complex) (M) TNF/TNF receptor inflammation n/d n/d modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) IC50 (modulator) (M) 39 703 4470566 TNF receptor 1ft4 2.7 × 10 –7 interaction biological role PDB (complex) K d (complex) (M) bromodomain/histone inflammation n/d n/d modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) IC50 (modulator) (M) 40 P9M 53054259 BRD2 4a9m 5.0 × 10 –7 41 A9N 72200779 BRD2 4a9n 1.5 × 10 –6 42 JQ1 46907787 BRD2 3oni 1.3 × 10 –7 b 43 JQ1 46907787 BRDT 4flp 1.9 × 10 –7 b 44 JQ1 46907787 BRD4 3mxf 4.9 × 10 –8 b 45 EAM 46943432 BRD4 3p5o 5.1 × 10 –8 b 46 I-BET151 52912189 BRD4 3zyu 1.0 × 10 –7 b interaction biological role PDB (complex) K d (complex) (M) integrin α-L/ICAM1 (CD-54) host–virus interaction 1nw9 2.0 × 10 –8 modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) IC50 (modulator) (M) 47 LA1 5326914 integrin α-L 1xuo 6.9 × 10 –8 48 2O7 16040268 integrin α-L 2o7n 1.5 × 10 –8 49 BQM 11712628 integrin α-L 3bqm 1.7 × 10 –9 50 E2M 24875322 integrin α-L 3e2m 0.4 × 10 –10 51 BJZ 11699447 integrin α-L 3m6f 2.5 × 10 –9 a Original references for the IC50 data were retrieved from the relevant PDB entries in the Protein Data Bank ( www.pdb.org ).
Discovery of highly potent p53-MDM2 antagonists and structural basis for anti-acute myeloid leukemia activities.
(2014) ACS Chem Biol 9
PubMed: 24405416 | PubMedCentral: PMC3985958 | DOI: 10.1021/cb400728e
For comparison, the indole ring of Trp23 from the p53-MDM2 complex (PDB ID: 1YCR) is aligned and shown in green sticks.
(B) Alignment of the p53 hot spot triad F 19 W 23 L 26 (magenta sticks, PDB ID: 1YCR) with MDM2-YH239.
Apoptosis therapy in cancer: the first single-molecule co-activating p53 and the translocator protein in glioblastoma.
(2014) Sci Rep 4
PubMed: 24756113 | PubMedCentral: PMC3996484 | DOI: 10.1038/srep04749
A superposition of all these structures on the alpha carbon atoms, using 1YCR as reference, shows that several of them, including 1YCR, lack the N-terminus residues 16–24 while others possess ... his region which forms (eg.
Besides the apo-protein NMR structure (PDB code: 1Z1M) and the X-ray structure of MDM2 bound to the transactivation domain of p53 (PDB code: 1YCR), several complexes of MDM2 with different small molecules are reported.
PubMed ID is not available.
Published in 2014
Starting with the p53–DNA complex (top, left, magenta protein, blue DNA), and moving in a clockwise direction, the Protein Data Bank 147 IDs and partner names are given as follows for the 14 c... mplexes: (1tsr – DNA), (1gzh – 53BP1), (1q2d – gcn5), (3sak – p53 (tetramerization domain)), (1xqh – set9), (1h26 – cyclin A), (1ma3 – sirtuin), (1jsp – CBP bromo domain), (1dt7 – s100ββ), (2h1l – sv40 Large T antigen), (1ycs – 53BP2), (2gs0 – PH), (1ycr – MDM2), and (2b3g – RPA70).
Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.
(2014) PLoS Comput Biol 10
PubMed: 25079060 | PubMedCentral: PMC4117425 | DOI: 10.1371/journal.pcbi.1003741
Target Structural data Docking-based druggability Protein flexibility Variation PDB ID RMSD ave (Å) [A] dock hit rate [B] DScore+ [A] [B] CDK2 1aq1 1.32 1.7 21% 11% 1buh 1.8 1.44 1.7 1dm2 1.8 ... .62 1.9 ER 1l2i 1.69 2.9 9% 7% 3ert 2.6 1.55 2.7 1err 2.0 1.61 2.8 HIV RT 1vrt 1.66 2.5 8% 13% 1rt1 1.5 1.75 2.3 1c1c 1.9 1.61 2.2 1rth 1.6 1.61 2.3 p38α 1a9u 1.00 1.8 49% 15% kinase 1kv1 3.8 1.16 2.1 1kv2 3.5 1.61 2.1 PPARγ 1fm6 1.46 2.9 13% 34% 1fm9 1.5 1.62 3.0 2prg 0.7 1.43 2.1 TK 1kim 1.58 2.7 12% 4% 1ki4 1.8 1.40 2.6 IL-2 1z92 0.13 * 107% 13% 1py2 2.6 0.62 * 1m48 2.5 0.62 * Bcl-XL 2bzw 1.04 2.4 21% 4% 2yxj 2.5 0.84 2.5 TNF 1tnf 0.95 2.4 1% 18% 2az5 2.9 0.96 2.0 MDM2 1ycr 0.45 2.5 69% 18% 1rv1 1.8 0.92 2.2 1t4e 1.6 0.66 2.1 HPV E2 1tue -0.24 * 323% 31% 1r6n 2.8 1.02 * Targets are from Huang and Jacobson  , and include all targets where at least two structures have an RMSD ave greater than 1.5 Å.
Target name PDB ID Ligand type Assigned druggability Crystal pocket Flexible model Dscore+ Volume Dscore+ Volume Bcl-xL 2bzw protein druggable 1.5 112 2.4 172 Bcl-2 2xa0 protein druggable 1.5 167 2.0 174 HDM2 1ycr protein druggable 1.7 165 2.5 175 TNFα 1tnf protein difficult 1.8 126 2.4 257 IL-2Rα 1z92 protein difficult 0.9 49 * * HPV E2 1tue protein difficult 0.8 57 * * ZipA 1f46 protein difficult 0.7 105 * * ZipA 1f47 protein difficult 0.9 141 * * Bcl-xL 2yxj cmpd druggable 1.8 141 2.5 239 Bcl-xL 3qkd cmpd druggable 1.9 132 2.1 195 Bcl-xL 4ehr cmpd druggable 1.4 100 2.4 175 Bcl-2 4aq3 cmpd druggable 1.7 113 2.3 220 HDM2 1rv1 cmpd druggable 1.7 147 2.2 178 HDM2 1t4e cmpd druggable 1.6 203 2.1 234 HDM2 3jzk cmpd druggable 1.6 204 1.9 184 HDM2 3lbk cmpd druggable 1.5 150 1.9 160 HDM2 3lbl cmpd druggable 2.0 224 2.2 218 HDM2 3tu1 cmpd druggable 1.5 221 1.9 172 HDM2 4dij cmpd druggable 1.6 192 1.8 207 HDM2 4ere cmpd druggable 1.8 165 2.5 172 TNFα 2az5 cmpd difficult 1.7 325 2.0 233 TNFR1 1ft4 cmpd difficult 1.2 330 * * IL-2Rα 1py2 cmpd difficult 1.2 66 * * IL-2Rα 1pw6 cmpd difficult 1.4 73 1.4 72 HPV E2 1r6n cmpd difficult 1.2 95 * * ZipA 1y2f cmpd difficult 0.9 91 * * ZipA 1y2g cmpd difficult 0.9 96 * * These targets have protein-protein co-crystal structures shown in the top half of the table, and corresponding protein-ligand co-crystal structures are shown in the bottom half.
Figure 1 Alignment of Mdm4 (green cartoon, PDB 3DAB) and Mdm2 (magenta cartoon PDB 1YCR) with the Mdm2 peptide (yellow cartoon and sticks) highlighting the similarities and differences of the two bind... ng sites (the Mdm4 binding p53 peptide is omitted for clarity).
Structure of a stapled peptide antagonist bound to nutlin-resistant Mdm2.
(2014) PLoS One 9
PubMed: 25115702 | PubMedCentral: PMC4130638 | DOI: 10.1371/journal.pone.0104914
Structure of Nutlin (magenta) bound to Mdm2 (left) with M62 highlighted in yellow (adapted from 1YCR).
It also positions the conserved p53-derived Mdm2 interaction motif (F19, W23, L26) into an identical orientation compared to the crystal structures elucidated for Mdm2 in complex with linear peptides either derived from the p53 WT sequence (PDB: 1YCR)  or the PMI variant selected for high affinity (PDB: 3EQS)  .
Orthogonal functionalisation of ?-helix mimetics.
(2014) Org Biomol Chem 12
PubMed: 25065821 | PubMedCentral: PMC4157654 | DOI: 10.1039/c4ob00915k
The p53/ h DM2 interaction represents a PPI under intense current investigation 37 ( Fig. 1b ); it exploits residues Phe19, Trp23 and Leu26 on the p53 transactivation domain bound in a helical conform... tion to h DM2 (PDB ID: ; 1YCR).
44 Fig. 1 Helix mimetics as inhibitors of PPIs: (a) schematic illustrating proteomimetic concept, (b) p53/ h DM2 interaction (PDB ID: ; 1YCR), (c) N - and (d) O -alkylated aromatic oligoamides, (e) schematic illustrating concept for orthogonal functionalisation.
Structural insights into the transcription-independent apoptotic pathway of p53.
(2014) BMB Rep 47
PubMed: 24499665 | PubMedCentral: PMC4163879 | DOI: null
(B) Crystal structure of the MDM2/p53TAD peptide (residues 15-29) complex (PDB code: 1YCR) (9) .
Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces.
PubMed: 25275445 | PubMedCentral: PMC4183424 | DOI: 10.1371/journal.pcbi.1003872
Protein-Protein Complex Receptor/Ligand Structures in PDB Model with highest BSSC c R d Unbound a Bound (Ligand) b MDM2/p53 1z1m (24) 1ycr (p53 peptide) Model 19 (2 nd ) 0.78 1rv1 (Nutlin-2) Model 19 ... 2 nd) 0.72 2lzg (piperidinone) Model 9 (1 st ) 0.77 PSD-95 PDZ1/CRIPT 1iu2 (50) 1rgr (peptide) Model 23 (1 st ) 0.92 MAGI-1 PDZ1/HPV16 E6 2kpk (20) 2kpl (peptide) Model 9 (3 rd ) 0.77 EDC3/DCP2 4a53 (20) 4a54 (peptide) Model 16 (2 nd ) 0.60 Bcl-xL/BAK, BAX, PUMA, BAD, etc. 2m03 (20) 2yxj (ABT-737) Model 3 (1 st ) 0.85 1bxl (BAK peptide) Model 3 (1 st ) 0.72 a The number in parenthesis indicates the number of structures in the NMR ensemble.
A. MDM2 bound to a p53 peptide (PDB ID 1ycr).
The accession codes are 1z1m, 1ycr, 1rv1, 2lzg, 1iu2, 1rgr, 2kpk, 2kpl, 4a53, 4a54, 2m03, 2yxj, and 1bxl.
Residues within 4 Å from the p53 peptide (PDB 1ycr) are marked with red dots.
Structural basis for inhibition of the MDM2:p53 interaction by an optimized MDM2-binding peptide selected with mRNA display.
PubMed: 25275651 | PubMedCentral: PMC4183577 | DOI: 10.1371/journal.pone.0109163
( A ) superpositions of MIP-MDM2 fusion (PDB ID = 2RUH), DI:MDM2 (3G03), PMI:MDM2 (3EQS), and p53 peptide:MDM2 (1YCR) in ribbons, viewed as in Fig. 2A, right.
Experimental Section Docking and Design Protocol in Rosetta The oxopiperazine dimer scaffold was initially docked by aligning Cβ atoms on the scaffold positions corresponding to hotspot residu... s on P53 (R 1 , Phe19, R 2 , Trp23, R 3 , Leu26) and HIF1α (R 1 , Leu818, R 2 , Leu822, R 4 , Gln824) using the PDB structure: 1YCR and 1L8C, respectively.
Published in 2015
MDM2 complexes To build models of the different MDM2 complexes, the following PDB structures were used as templates: 1YCR (p53) [ 16 ], 4HG7 (Nutlin-3a) [ 21 ], 1T4E (Bzd) [ 23 ], and 4HBM (Pip2) [ 24... ].
Publication Year: 2015
RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.