Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 29

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Projections for fast protein structure retrieval.

(2006) BMC Bioinformatics 7 Suppl 5

PubMed: 17254310 | PubMedCentral: PMC1764482 | DOI: 10.1186/1471-2105-7-S5-S5

Next six entries in Table 2 give results from comparison of 2HCK and 2SRC with their individual domains.

Publication Year: 2006

Comparison of protein structures by growing neighborhood alignments.

(2007) BMC Bioinformatics 8

PubMed: 17338826 | PubMedCentral: PMC1828169 | DOI: 10.1186/1471-2105-8-77

In order to test the current programs' ability of detecting such similarities, we tested them for detecting the 3 individual domains in 2 multi-domain proteins, e.g. [PDB: 2HCK ] and [PDB: 2SRC ], tak... n from [ 12 ].

Publication Year: 2007

Recruitment of rare 3-grams at functional sites: is this a mechanism for increasing enzyme specificity?

(2007) BMC Bioinformatics 8

PubMed: 17598909 | PubMedCentral: PMC1950313 | DOI: 10.1186/1471-2105-8-226

c-Src inactive conformation (PDB:2SRC [58]) is shown as a ribbon diagram (white), the AMP-PNP as a stick model (orange), the phosphotyrosines Y416 and Y527 in space-filling representation, and SH2-kin... se domain linker (wheat).

Publication Year: 2007

A multi-template combination algorithm for protein comparative modeling.

(2008) BMC Struct Biol 8

PubMed: 18366648 | PubMedCentral: PMC2311309 | DOI: 10.1186/1472-6807-8-18

The RMSD between other three significant templates (2SRC, 1Y57, 1KSW) and the experimental structure is 3.22 Å for 250-residue aligned region, 2.33 Å for 262-residue aligned region, an... 3.20 Å for 250-residue aligned region respectively.

The RMSD between the model and the experimental structure is 2.63 Å for 271-residue long alignment, which is better than two templates (2SRC and 1KSW), but worse than the best template (1JPA).

Publication Year: 2008

Activation of tyrosine kinases by mutation of the gatekeeper threonine.

(2008) Nat Struct Mol Biol 15

PubMed: 18794843 | PubMedCentral: PMC2575426 | DOI: 10.1038/nsmb.1486

( b ) The inactive conformation of chicken c-SRC (PDB 2SRC), colored as in a .

The structures were solved by molecular replacement using the kinase domain of chicken c-SRC residues 250–533 (PDB 2SRC) 24 with the C helix and the activation loop deleted as a search model in the program Phaser 54 .

Publication Year: 2008

Analysis of the impact of solvent on contacts prediction in proteins.

(2009) BMC Struct Biol 9

PubMed: 19368710 | PubMedCentral: PMC2676287 | DOI: 10.1186/1472-6807-9-22

Reference structure used is PDB ID 2SRC .

Interacting partners PFAM ID1/ID2 PDB ID a N b % iden c L 1 d L 2 e X d dry f Opt Xd α g X d wet | opt α h Tyrosine kinase SH3/SH2 domains PF00018/PF00017 2SRC 19 35 57 83 1.86 0.2 3.25 Alcohol dehydrogenase N-/C-domains PF08240/PF00107 1ADG 89 23 128 143 3.52 0.2 3.64 Mg superoxide dismutase N-/C-domains PF00081/PF02777 1AP5 23 44 82 107 4.76 0.2 5.04 Immunoglobulin heavy/light chains PF00047/PF00047 12E8 116 36 107 114 13.56 0 13.56 Ortnithine transferase N-/C-domains PF02729/PF00185 1DUV 20 30 142 178 4.47 0.1 4.94 NFKB factor RHD/TIG domains PF00554/PF01833 1SVC 21 40 199 100 4.56 0.5 4.62 STAT alpha/binding domains PF01017/PF02864 1BF5 32 38 180 251 4.30 0.2 4.42 Mur-ligase catalytic/C-terminal domains PF01225/PF08245 1E8C 26 25 82 208 1.84 0.1 2.12 Dynamin central/N-domains PF00350/PF01031 2AKA 32 40 174 89 0.04 0.2 0.14 Trk C-/N-domains PF02254/PF02080 1LNQ 42 20 114 72 0.53 1 0.78 a PDB ID of the reference structure; b Number of sequences in the multiple sequence alignment; c Average percentage of sequences pairwise similarity; d, e Lengths of the reference sequences; f Values for α = 0; g α value corresponding to the highest X d ; h X d highest value.

Publication Year: 2009

SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns.

(2009) Nucleic Acids Res 37

PubMed: 19406922 | PubMedCentral: PMC2703984 | DOI: 10.1093/nar/gkp308

However, a user needs to input only a PDB code, e.g. 2src.

Major advantages of the SplitPocket system are: first, it is fully automatic and its only input is the PDB codes (e.g. 2src and 1ouk.

Publication Year: 2009

Optimal assignment methods for ligand-based virtual screening.

(2009) J Cheminform 1

PubMed: 20150995 | PubMedCentral: PMC2820492 | DOI: 10.1186/1758-2946-1-14

target number actives number decoys number clusters a PDB code b ace c 46 1796 19 p 1o86 ache d 100 3859 18 1eve cdk2 e 47 2070 32 1ckp cox2 f 212 12606 44 1cx2 egfr g 365 15560 40 1m17 fxa h 64 2092 ... 9 1f0r hivrt i 34 1494 17 1rt1 inha j 57 2707 23 1p44 p38 k 137 6779 20 1kv2 pde5 l 26 1698 22 1xp0 pdgfrb m 124 5603 22 1t46 src n 98 5679 21 2src vegfr2 o 48 2712 31 1fgi Overview of the used data sets containing the number of actives, decoys, different chemotype clusters, and the PDB code of the complexed crystal structure which contains the search query.

Publication Year: 2009

Application of 3D Zernike descriptors to shape-based ligand similarity searching.

(2009) J Cheminform 1

PubMed: 20150998 | PubMedCentral: PMC2820497 | DOI: 10.1186/1758-2946-1-19

Target PDB Actives Decoys Decoys per active angiotensin-converting enzyme (ace) 1o86 46 1796 39.04 acetylcholinesterase (ache) 1eve 100 3859 38.59 cyclin-dependent kinase 2(cdk2) 1ckp 47 2070 44.04 cy... looxygenase-2(cox2) 1cx2 212 12606 59.46 epidermal growth factor receptor(egfr) 1m17 365 15560 42.63 factor Xa(fxa) 1f0r 64 2092 32.69 HIV reverse transcriptase(hivrt) 1rt1 34 1494 43.94 enoyl ACP reductase(inha) 1p44 57 2707 47.49 P38 mitogen activated protein(p38) 1kv2 137 6779 49.48 phosphodiesterase(pde5) 1xp0 26 1698 65.31 platelet derived growth factor receptor kinase(pdgfrb) 1t46 124 5603 45.19 tyrosine kinase SRC(src) 2src 98 5679 57.95 vascular endothelial growth factor receptor(vegfr2) 1fgi 48 2712 56.5 The third dataset from the National Cancer Institute (NCI) consists of 42,687 compounds derived from an assay measuring protection from HIV-1 infection of human CEM cells [ 57 ].

Publication Year: 2009

Reciprocally coupled residues crucial for protein kinase Pak2 activity calculated by statistical coupling analysis.

(2010) PLoS One 5

PubMed: 20209159 | PubMedCentral: PMC2830475 | DOI: 10.1371/journal.pone.0009455

PDB and 2SRC.

PDB (PKA) [24] and 2SRC.

The statistical coupling residues of Src are shown on the tertiary structure (2SRC.

These residues were superimposed to the structure of Src (2SRC.

Publication Year: 2010

Control of genetically prescribed protein tyrosine kinase activities by environment-linked redox reactions.

(2011) Enzyme Res 2011

PubMed: 21755044 | PubMedCentral: PMC3132499 | DOI: 10.4061/2011/896567

Primary and tertiary structures of c-SRC (PDB 2SRC) and c-RET (PDB 2IVS) are deduced from the data in Protein Data Bank (PDB).

Publication Year: 2011

Using multiple microenvironments to find similar ligand-binding sites: application to kinase inhibitor binding.

(2011) PLoS Comput Biol 7

PubMed: 22219723 | PubMedCentral: PMC3248393 | DOI: 10.1371/journal.pcbi.1002326

The first row is structures of SRC bound with ANP (PDB ID: 2src) and a drug-like inhibitor (PDB ID is 3en7 and ligand PDB code is ABJ).

Publication Year: 2011

Highly specific, bisubstrate-competitive Src inhibitors from DNA-templated macrocycles.

(2012) Nat Chem Biol 8

PubMed: 22344177 | PubMedCentral: PMC3307835 | DOI: 10.1038/nchembio.792

44 The structure was phased by molecular replacement using the kinase domain of inactive c-Src (PDB: 2SRC) 45 (residues 250-533) without the αC-helix (residues 298-310) and activation loop (re... idues 400-425) as a search model in Phaser 40 The model of the structure was built in Coot 42 and refined in PHENIX.

Publication Year: 2012

Structural analysis of Staphylococcus aureus serine/threonine kinase PknB.

(2012) PLoS One 7

PubMed: 22701750 | PubMedCentral: PMC3372466 | DOI: 10.1371/journal.pone.0039136

It was superimposed onto the kinase structures of active PKA (grey, PDB ID: 1ATP [35] ) and inactive c-Src (purple, PDB ID: 2SRC [36] ) using C-lobe residues 100–250.

Structure-based sequence alignment of the S. aureus PknB kinase domain with the kinase domains of B. subtilis PrkC (no structure available), M. tuberculosis PknB (PDB ID: 1MRU [24] ), murine cAMP dependent Protein Kinase A (PDB ID: 1ATP [35] ; PDB ID: 1CTP [34] ) and human tyrosine protein kinase c-Src (PDB ID: 2SRC [36] ).

PknB SA-KD is in an inactive conformation In order to determine whether the structure of PknB SA-KD is in an active or an inactive conformation, we have compared it with the following kinase structures: (i) PknB of M. tuberculosis , which is the first reported structure of a bacterial STK (PDB ID: 1O6Y [23] and 1MRU [24] ; (ii) cAMP-dependent protein kinase A (PKA) in an open conformation (PDB ID: 1CTP [34] ); (iii) a closed, active PKA structure with bound ATP (PDB ID: 1ATP [35] ); and (iv) human c-Src, a tyrosine kinase in the autoinhibited conformation (PDB ID: 2SRC [36] ).

The kinase domain of c-Src (PDB ID: 2SRC [36] ) is shown in purple.

Publication Year: 2012

Structure of WbdD: a bifunctional kinase and methyltransferase that regulates the chain length of the O antigen in Escherichia coli O9a.

(2012) Mol Microbiol 86

PubMed: 22970759 | PubMedCentral: PMC3482155 | DOI: 10.1111/mmi.12014

The DALI server ( Holm and Rosenström, 2010 ) identifies a strong structural similarity to well-studied eukaryotic kinases including the Src kinase [PDB-id: 2SRC, Z-score: 12.2, r.m.s.d.: 3.3 ... #x000c5;, length of alignment: 182 residues ( Xu et al .

Interestingly, Src (PDB: 2SRC) superimposes more closely on WbdD459 (r.m.s. = 3.3 Å (350 Cα atoms) than on WbdD556 [r.m.s. = 5.6 Å (350 Cα atoms)].

Publication Year: 2012

Virtual screening of specific insulin-like growth factor 1 receptor (IGF1R) inhibitors from the National Cancer Institute (NCI) molecular database.

(2012) Int J Mol Sci 13

PubMed: 23242155 | PubMedCentral: PMC3546745 | DOI: 10.3390/ijms131217185

The receptors and PDB IDs were CDK2 (1ckp), EGFr (1m17), FGFr1 (1agw), P38_MAP (1kv2), PDGFrb (model), SRC (2src), and VEGFr2 (1vr2).

Publication Year: 2012

Src activation by ?-adrenoreceptors is a key switch for tumour metastasis.

(2013) Nat Commun 4

PubMed: 23360994 | PubMedCentral: PMC3561638 | DOI: 10.1038/ncomms2413

Figure 4 Interaction between pS17 and Src results in conformational changes that expose Y419 (a) Inactive form of the protein obtained from the protein data bank (PDB code: 2SRC).

First, we obtained the atomic coordinates of c-Src from the Protein Data Bank (Code:2SRC) 12 , and proceeded to eliminate phospho-aminophosphonic acid-adenylate ester (ANP) and water molecules, leaving Src in its inactive form ( Figure 4a ).

Publication Year: 2013

Distal loop flexibility of a regulatory domain modulates dynamics and activity of C-terminal SRC kinase (csk).

(2013) PLoS Comput Biol 9

PubMed: 24039559 | PubMedCentral: PMC3764022 | DOI: 10.1371/journal.pcbi.1003188

Structural alignment was performed in PyMol using PDB entries 2ETZ, 2SRC, and 3EAC for Itk, Src, and Csk, respectively.

Publication Year: 2013

An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility.

(2013) BMC Struct Biol 13 Suppl 1

PubMed: 24564934 | PubMedCentral: PMC3952246 | DOI: 10.1186/1472-6807-13-S1-S10

Enolase Superfamily (homogeneous): Enolases: 1e9i , 1iyx , 1pdy , 2pa6 , 2xsx , 2xsx Enolase Superfamily (homogeneous, redundant): Enolases: 1ebh , 1els , 1nel , 2al2 , 3enl , 7enl , 1te6 , 1ebg , 1on... Tyrosine Kinases (homogeneous): Small Gatekeeper residue: 1qcf , 1fgi , 1fpu , 1fvr , 1gjo , 1irk , 1k2p , 1m14 , 1m7n , 1qpc , 1r0p , 1t45 , 1u4d , 1yvj , 1ywn , 2src Tyrosine Kinases (homogeneous, redundant): Small Gatekeeper residue: 2hz4 , 2e2b , 2hyy , 2hz0 , 2hzn , 2hzi , 2xyn , 2hmi , 3kf4 , 3kfa , 3ms9 , 3mss Enolase Superfamily (heterogeneous): Enolases: 1e9i , 1ebh , 1iyx , 1pdy , 1te6 , 2pa6 , 2xsx , 3otr , Mandelate Racemase: 2ox4 , Muconate Lactonizing Enzyme: 2pgw , 2zad Tyrosine Kinases (heterogeneous): Small Gatekeeper residue: 2hz4 Large Gatekeeper residue: 1fvr , 1luf , 1rjb , 1sm2 , 1snu , 1snx Bolded structures were selected as templates.

Publication Year: 2013

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4114474

The DUD proteins include acetycholinesterase AChE (PDB code: 1EVE), human androgen receptor AR (PDB code: 1XQ2), human cyclin-dependent kinase 2 CDK2 (PDB code: 1CKP), human epidermal growth factor re... eptor EGFR (PDB code: 1M17), human mitogen-activated protein kinase 14 known as p38 (PDB code: 1KV2), human proto-oncogene tyrosine-protein kinase Src (PDB code: 2SRC), and cationic trypsin (PDB code: 1BJU).

Publication Year: 2014

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4136698

(A) SFK activity is allosterically modulated by engagement of the SH2 and SH3 regulatory domains (PDB: 2SRC).

Publication Year: 2014

Differential sensitivity of Src-family kinases to activation by SH3 domain displacement.

(2014) PLoS One 9

PubMed: 25144189 | PubMedCentral: PMC4140816 | DOI: 10.1371/journal.pone.0105629

The analogous interaction of the Src SH3 domain with the SH2-kinase linker from the inactive structure of c-Src is shown on the right (PDB: 2SRC) [8] .

Materials and Methods Cloning, expression, and purification of recombinant SFK domains The coding sequences for the isolated SH3 and SH2 domains of human c-Src, Fyn, Hck, and Lyn, and the isolated kinase domains (KD) of c-Src and Hck(corresponding to residues 81–142 (SH3), 143–244 (SH2), and 251–533 (KD) of c-Src, numbering according to PDB ID: 2SRC) were amplified by PCR and subcloned into the bacterial expression vector pET21a (EMD Millipore) using NdeI and XhoI restriction sites.

A) ESI-MS/MS spectra of Src-YEEI peptic peptide YFTSTESQpY 527 EEIP ([M+H] +  = 1683.68 Da), which is derived from the C-terminal tail, indicates that Tyr527 is phosphorylated (numbering as per crystal structure of c-Src; PDB ID: 2SRC).

A) ESI-MS/MS spectra of Src-YEEI peptic peptide IEDNEpY 416 TARQGAKF ([M+H] +  = 1721.75 Da), derived from the activation loop, indicates that Tyr416 is phosphorylated (numbering as per crystal structure of c-Src; PDB ID: 2SRC).

Phosphorylation of Tyr416 (all residue numbering as per the structure of c-Src; PDB code 2SRC) in the activation loop stabilizes the active conformation of the kinase domain.

A) Crystal structure of inactive c-Src (PDB: 2SRC) [8] showing the intramolecular interactions necessary for downregulation of kinase activity.

Publication Year: 2014

c-Src binds to the cancer drug Ruxolitinib with an active conformation.

(2014) PLoS One 9

PubMed: 25197973 | PubMedCentral: PMC4157781 | DOI: 10.1371/journal.pone.0106225

In the DFG-intermediate conformation ( Figure 2D , pdb 2SRC), the DFG-motif adopts a conformation between the above two conformations.

Initial phase determination was performed by molecular replacement with Phaser from the CCP4 package [25] , using chain A of a previously solved c-Src structure(PDB code 2SRC) [26] as the search model.

(A) active Lck DFG-in conformation (pdb: 3LCK); (B) active c-Src T338I DFG-in conformation (pdb: 3DQW); (C) active c-Src DFG-in conformation in Src/Ruxolitinib complex (this work); (D) inactive c-Src in the Src/CDK conformation, DFG-intermediate (pdb: 2SRC); (E) inactive c-Src DFG-out conformation in Src/Imatinib complex (pdb: 2OIQ).

Publication Year: 2014

Exploiting holistic approaches to model specificity in protein phosphorylation.

(2014) Front Genet 5

PubMed: 25324856 | PubMedCentral: PMC4179730 | DOI: 10.3389/fgene.2014.00315

The protein interaction domains SH3 and SH2 domains in Src are fundamental for Src activation (inactive Src: pdb 2SRC), as shown in the cartoon in the middle (Xu et al., 1999 ).

Publication Year: 2014

A dynamically coupled allosteric network underlies binding cooperativity in Src kinase.

(2015) Nat Commun 6

PubMed: 25600932 | PubMedCentral: PMC4300553 | DOI: 10.1038/ncomms6939

Without using any crystal structure information about the αC-out conformation, the simulations produced the correct αC-out conformation, in which the helix is ~2 Å back... one root mean squared deviation (r.m.s.d.) from the inactive conformation as captured in PDB entry 2SRC ( Fig. 1c , Plot N and Supplementary Fig. 2a , Plot N), and ~8 Å backbone r.m.s.d. away from the initial (active) αC-in conformation.

( c ) Prepared using a snapshot from a simulation, but the key features highlighted (for example, the positions of Trp260 and the Glu310-Arg409 salt bridge) are also seen in the crystal structure of inactive Src kinase (PDB 2SRC).

The structure at the end of the simulation resembles that in the crystal structure (red) of autoinhibited Src kinase (Experiment—Inactive, PDB entry 2SRC).

Publication Year: 2015

Markov state models provide insights into dynamic modulation of protein function.

(2015) Acc Chem Res 48

PubMed: 25625937 | PubMedCentral: PMC4333613 | DOI: 10.1021/ar5002999

(B) The projection of HMM states onto two degrees of freedom representing the RMSD of activation loop from inactive crystal structure (2SRC) and switching of the electrostatic network, respectively.

Publication Year: 2015

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4350284

Six tyrosine residues were included in the analysis, which are putatively surface exposed in the structure of cSrc (PDB: 2SRC) or have been described to be phosphorylated (Figure  2 A) [ 23 , ... 4 ].

Publication Year: 2015

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4384635

The SH3 domain was built by comparison with the c-Src SH3 domain (PDB ID 2SRC).

We generated a homology model for the SH2 domain from the SH2 domains present in PDB entries for Src, Hck and Abl containing SH3-SH2-kinase constructs (PDB IDs: 1FMK, 1KSW, 2SRC, 2PTK, 1AD5, 1QCF, 2HCK, 1OPK).

Publication Year: 2015

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4465921

To sample the conformational landscape more efficiently, we start a large number of relatively short simulations from configurations along an optimal pathway connecting the active (pdb id:1Y57 29 ) an... inactive (pdb id:2SRC 30 ) states determined using the string method with swarm-of-trajectories.

Methods Generation of Initial Pathway Using String Method The inactive (PDB ID: 2SRC) 30 and active (PDB ID: 1Y57) 29 x-ray structures of human c-src kinase were used as the two end-point conformations for the generation of the Minimum Free Energy Pathway (MFEP).

Publication Year: 2014