Citations in PubMed

Primary Citation PubMed: 17638903 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 5

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

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.

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The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins.

(2007) J Struct Funct Genomics 8

PubMed: 17932789 | PubMedCentral: PMC2140095 | DOI: 10.1007/s10969-007-9027-2

Cancer e Other-NAK STK10 2J7T 2.0 SU11274 Not known STE DAPK3 2J90 2.0 Pyridone 6 Cancer, Inflammation CAMK CAMK1G 2JAM 1.7 SU11652 Not known CAMK CAMK1D 2JC6 2.5 GSK inhibitor XIII Genetic CAMK a PAK... also deposited as an apo-structure in two different spacegroups: 2BVA, 2J01 b Structures with different inhibitors and substrate: PIM1: 2BIK, 2BZH,2BZI, 2BZJ, 2BZK, 2C3I, 2BIL, 2J2I; SLK: 2JA0 c CLK3 also deposited as phosphorylated protein: pdb-code: 2EXE.

Publication Year: 2007


Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors.

(2011) PLoS One 6

PubMed: 21572516 | PubMedCentral: PMC3084719 | DOI: 10.1371/journal.pone.0018934

(A) Bound PDB id Sec str Start backbone-RMSD ∫ Start ϕ/ψ RMSD ∫ Best backbone- iRMSD † Top-10 backbone-iRMSD ‡ Rank of first near-native cluster Hexamer... all-atom top-10 * 1NVR a β + C 1.2 Å 23° 0.2 Å 0.5 Å 1 0.9 Å b 2FMF c A 16.1 Å 131° 0.4 Å 0.5 Å 7 0.6 Å 2O9V c C 5.5 Å 49° 0.4 Å 0.6 Å 1 0.4 Å 2P1K β + C 6.1 Å 61° 0.5 Å 0.6 Å 1 0.6 Å 1RXZ β + C 8.9 Å 80° 0.7 Å 0.7 Å 1 0.9 Å 2R7G α + C 11.2 Å 106° 0.8 Å 0.8 Å 7 1.1 Å 1AWR C 5.3 Å 57° 0.8 Å 0.9 Å 1 1.6 Å 2FNT C 1.4 Å 47° 0.4 Å 1.0 Å 1 2.0 Å 3D1E C 1.6 Å 67° 0.7 Å 1.1 Å 1 1.3 Å 2B1Z A 8.9 Å 124° 0.4 Å 1.2 Å 1 2.2 Å 1T7R A 13.4 Å 128° 0.7 Å 1.2 Å 3 0.8 Å 1N7F c β + C 3.8 Å 52° 0.3 Å 1.4 Å 1 0.8 Å 1ER8 C 6.0 Å 52° 0.8 Å 1.4 Å 1 1.9 Å 1W9E β + C 1.2 Å 39° 0.5 Å 1.5 Å 1 2.7 Å b 2VJ0 C 5.3 Å 72° 1.2 Å 1.5 Å 1 1.4 Å 1Z9O C 6.9 Å 56° 1.6 Å 1.6 Å 2 1.4 Å 2P54 α + C 13.0 Å 120° 0.8 Å 1.8 Å 2 2.2 Å 1NLN β + C 11.7 Å 27° 0.7 Å 2.0 Å 5 1.7 Å 2A3I c α + C 17.3 Å 115° 0.7 Å 2.1 Å 314 2.2 Å 1SSH C 8.4 Å 50° 0.9 Å 3.1 Å 51 2.7 Å 2J6F C 7.4 Å 44° 1.7 Å 5.7 Å >500 7.2 Å 1KL3 α + C 9.4 Å 93° 0.9 Å 5.8 Å >500 6.5 Å 1TW6 C 3.3 Å 46° 1.8 Å 5.9 Å >500 6.5 Å 2C3I C 13.0 Å 70° 1.5 Å 6.0 Å 308 4.7 Å 2FGR c C 7.3 Å 79° 1.3 Å 8.6 Å >500 8.6 Å 1QKZ C 13.51Å 78° 3.1 Å 8.8 Å None 4.5 Å Performance of peptide modeling onto Bound (A) and Unbound (B) protein receptor structures.

Unbound PDB id Unbound receptor Cα- iRMSD Sec str Start backbone-RMSD ∫ Start ϕ/ψ-RMSD ∫ Best backbone- iRMSD† Top-10 backbone-iRMSD‡ Rank of first near-native cluster Hexamer all-atom top-10 * 1NVR 0.3 Å β + C 1.2 Å 23° 0.2 Å 0.4 Å 2 1.1 Å b 2O9V c 0.3 Å C 5.5 Å 49° 0.4 Å 0.6 Å 1 0.6 Å 1N7F c 0.4 Å β + C 3.8 Å 52° 0.8 Å 1.0 Å 9 1.2 Å 2VJ0 0.3 Å C 5.3 Å 72° 1.2 Å 1.4 Å 8 1.8 Å 1AWR 0.3 Å C 5.3 Å 57° 0.9 Å 1.4 Å 2 2.0 Å 2A3I c 0.3 Å α + C 17.3 Å 115° 0.7 Å 1.5 Å 10 1.7 Å 1W9E 0.6 Å β + C 1.2 Å 39° 0.7 Å 1.9 Å 1 2.8 Å b 1T7R 0.4 Å α 13.4 Å 128° 0.7 Å 2.6 Å 28 4.1 Å 1SSH 0.7 Å C 8.4 Å 50° 1.1 Å 3.2 Å 22 4.2 Å 2C3I 0.2 Å C 13.0 Å 70° 1.8 Å 3.7 Å 299 6.4 Å 1RXZ c 1.5 Å β + C 8.9 Å 80° 1.9 Å 4.3 Å >500 2.1 Å 2FMF 0.5 Å α 16.1 Å 131° 0.4 Å 5.0 Å 29 3.5 Å 2P54 0.7 Å α + C 13.0 Å 120° 2.2 Å 9.7 Å None 8.1 Å 2FGR c 0.3 Å C 7.3 Å 79° 1.6 Å 10.1 Å >500 9.1 Å Performance of peptide modeling onto Bound (A) and Unbound (B) protein receptor structures.

Publication Year: 2011


The design and application of target-focused compound libraries.

(2011) Comb Chem High Throughput Screen 14

PubMed: 21521154 | PubMedCentral: PMC3182092 | DOI: null

Table 1 The Kinases with Associated Classification that Make Up the BioFocus Library Evaluation Panel Kinase Crystal Structure Used (PDB Access Code) Classification PIM-1 2C3I Inactive conformation ME... 2 1S9I Active conformation P38α 1WBS Inactive conformation AurA 2C6E Inactive conformation JNK 2GMX Active conformation FGFR 2FGI Active conformation HCK 1QCF Active conformation Table 2 An Example Sub-Pocket of Five Different Channels, Showing how the Amino Acids Occupying these Defined Residue Positions Determine the Property of the Corresponding Ligand Moiety Channel Residue Position in Sub-Pocket (Based on KCSA Numbering) Property of Ligand Moiety Recognized 75 99 100 100 103 104 107 Kir1.4 T T T T E I T Basic amine hERG S G S S Y A F Basic amine/aromatic ring Cav1.1 D2 D3 G G N A L L F H-bonding Kv1.1 T G V V I A V Lipophilic Kvlqt1 T A V V F A A Lipophilic Table 3 IC50s (in µM) of Two SFI01 Compounds Against 4 VGICs KCNQ2/3 IK Cav Nav1.5 Compound A >100 >100 1.74 23.64 Compound B 1.6 >100 11.66 >100

In 1999, the BioFocus group pioneered the design and commercial production of novel target-focused libraries and, since its SoftFocus ® range of libraries were first made available, they have contributed significantly to clients’ drug discovery efforts, leading to more than 100 patent filings [ 7 ] and nine published co-crystal structures, available from the Protein Data Bank (PDB) [ 8 ]: PDB codes 2R3A, 2R3G [ 9 ], 3F2A [ 10 ], 2C3I [ 11 ], 2PMN [ 12 ], 3IW8 [ 13 ], 3E7V, 3F2N and 3BQR.

(2) Selection of crystallized SFK library compounds in the public domain ( a ) hinge binding: SFK03 compound bound to CDK2 (PDB code 2R3F); ( b ) DFG-out binding: SFK48 compound bound to p38α [ 13 ] (PDB code 3IW8); ( c ) invariant lysine binding: SFK33 compound bound to PIM-1 [ 11 ] (PDB code 2C3I).

Publication Year: 2011


Fragment-hopping-based discovery of a novel chemical series of proto-oncogene PIM-1 kinase inhibitors.

(2012) PLoS One 7

PubMed: 23115625 | PubMedCentral: PMC3480357 | DOI: 10.1371/journal.pone.0045964

Structural Information The crystal structure of PIM-1 determined in complex with compound 2 (2C3I.

a) Imidazopyridazine ligand 2 bound to PIM-1 in the crystal structure, where explicit hydrogen bonds involved in the binding are highlighted; b) Bidimensional (2D) interaction map for the complex PIM-1 : compound 2 extracted from 2C3I.

The Protein Data Bank (PDB) code is 2C3I.

For validation purposes, we compared the data for compound 2 docked to PIM-1 with the corresponding crystal structure [pdb entry 2C3I.

Publication Year: 2012


Crystal structure of pim1 kinase in complex with a pyrido[4,3-d]pyrimidine derivative suggests a unique binding mode.

(2013) PLoS One 8

PubMed: 23936194 | PubMedCentral: PMC3729456 | DOI: 10.1371/journal.pone.0070358

PDB codes 2BIL (purple), 2C3I (cyan), 3CY2 (light pink) and 3MA3 (ivory) were used for structural comparison.

In the inhibitor-bound Pim1 structure, pimtide yielded a structure identical to previously reported Pim1 structures (PDB codes 2BIL, 2BZK [23] , 2C3I [24] , 3CY2 [25] , and 3MA3 [26] ), wherein the pimtide was modeled into the substrate-binding pocket ( Fig. 3A ).

Publication Year: 2013