1YOM

Crystal structure of Src kinase domain in complex with Purvalanol A

Structural Biology Knowledgebase: 1YOM SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YOM

Classification: TRANSFERASE

Total Structure Weight: 65678.80

Macromolecule Entities
Molecule Chains Length Organism Details
Proto-oncogene tyrosine-protein kinase Src A, B 283 Homo sapiens EC#: 2.7.10.2 IUBMB
Fragment: Src kinase domain
Mutation: S344N, A369S, Y418W
Gene Name(s): SRC Gene View SRC1

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
P01
Query on P01

A, B 2-({6-[(3-CHLOROPHENYL)AMINO]-9-ISOPROPYL- 9H-PURIN-2-YL}AMINO)-3-METHYLBUTAN-1-OL
PURVALANOL A (Synonym)
C19 H25 Cl N6 O
PMXCMJLOPOFPBT-HNNXBMFYSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
P01 IC50: 240 nM (98) BindingDB

N/A in BindingMoad
N/A in PDBbind

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 = 41.70 α = 100.61
b = 63.08 β = 88.86
c = 74.06 γ = 89.89

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-27
  • Released Date: 2006-01-27
  • Deposition author(s): Breitenlechner, C.B., Kairies, N.A., Honold, K., Scheiblich, S., Koll, H., Greiter, E., Koch, S., Schaefer, W., Huber, R., Engh, R.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4