1YOM

Crystal structure of Src kinase domain in complex with Purvalanol A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structures of active SRC kinase domain complexes

Breitenlechner, C.B., Kairies, N.A., Honold, K., Scheiblich, S., Koll, H., Greiter, E., Koch, S., Schaefer, W., Huber, R., Engh, R.A.

(2005) J.Mol.Biol. 353: 222-231

  • DOI: 10.1016/j.jmb.2005.08.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • c-Src was the first proto-oncoprotein to be identified, and has become the focus of many drug discovery programs. Src structures of a major inactive form have shown how the protein kinase is rigidified by several interdomain interactions; active conf ...

    c-Src was the first proto-oncoprotein to be identified, and has become the focus of many drug discovery programs. Src structures of a major inactive form have shown how the protein kinase is rigidified by several interdomain interactions; active configurations of Src are generated by release from this "assembled" or "bundled" form. Despite the importance of Src as a drug target, there is relatively little structural information available regarding the presumably more flexible active forms. Here we report three crystal structures of a dimeric active c-Src kinase domain, in an apo and two ligand complexed forms, with resolutions ranging from 2.9A to 1.95A. The structures show how the kinase domain, in the absence of the rigidifying interdomain interactions of the inactivation state, adopts a more open and flexible conformation. The ATP site inhibitor CGP77675 binds to the protein kinase with canonical hinge hydrogen bonds and also to the c-Src specific threonine 340. In contrast to purvalanol B binding in CDK2, purvalanol A binds in c-Src with a conformational change in a more open ATP pocket.

    Organizational Affiliation: 

    Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, 82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase Src
A, B
283Homo sapiensMutation(s): 3 
Gene Names: SRC (SRC1)
EC: 2.7.10.2
Find proteins for P12931 (Homo sapiens)
Go to Gene View: SRC
Go to UniProtKB:  P12931
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P01
Query on P01
Download SDF File 
Download CCD File 
A, B
2-({6-[(3-CHLOROPHENYL)AMINO]-9-ISOPROPYL-9H-PURIN-2-YL}AMINO)-3-METHYLBUTAN-1-OL
PURVALANOL A
C19 H25 Cl N6 O
PMXCMJLOPOFPBT-HNNXBMFYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P01IC50: 240 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.217 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.698α = 100.61
b = 63.078β = 88.86
c = 74.055γ = 89.89
Software Package:
Software NamePurpose
REFMACrefinement
CCP4data scaling
AMoREphasing
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-27
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance