4BKJ

Crystal structure of the human DDR1 kinase domain in complex with imatinib

Structural Biology Knowledgebase: 4BKJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.176
  • R-Value Work: 0.156

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4BKJ

Classification: TRANSFERASE

Total Structure Weight: 73675.31

Macromolecule Entities
Molecule Chains Length Organism Details
EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1 A, B 315 Homo sapiens EC#: 2.7.10.1 IUBMB
Fragment: KINASE DOMAIN, RESDIUES 564-876
Gene Name(s): DDR1 Gene View CAK EDDR1 NEP NTRK4 PTK3A RTK6 TRKE

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

A, B 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL- 3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]- BENZAMIDE
STI-571;IMATINIB (Synonym)
C29 H31 N7 O
KTUFNOKKBVMGRW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
STI N/A in BindingDB
IC50: 41 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.176
  • R-Value Work: 0.156
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 60.07 α = 90.00
b = 60.07 β = 90.00
c = 180.57 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-25
  • Released Date: 2013-05-22
  • Deposition author(s): Canning, P., Elkins, J.M., Goubin, S., Mahajan, P., Krojer, T., Vollmar, M., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.

Revision History

  • 2014-06-18
    Type: Citation | Details: JRNL
  • 2014-05-07
    Type: Citation | Details: JRNL
  • 2014-04-23
    Type: Citation | Details: JRNL