7AYM

Structure of DDR2 Kinase domain in complex with IBZ3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Structure of DDR2 Kinase domain in complex with IBZ3

Nawrotek, A., Talagas, A., Vuillard, L.M., Miallau, L.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Discoidin domain-containing receptor 2,Epithelial discoidin domain-containing receptor 1337Homo sapiensMutation(s): 2 
Gene Names: 
DDR2, NTRKR3, TKT, TYRO10, DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A...
DDR2, NTRKR3, TKT, TYRO10, DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE

EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16832 (Homo sapiens)
Explore Q16832 
Go to UniProtKB:  Q16832
PHAROS:  Q16832
GTEx:  ENSG00000162733 
Find proteins for Q08345 (Homo sapiens)
Explore Q08345 
Go to UniProtKB:  Q08345
PHAROS:  Q08345
GTEx:  ENSG00000204580 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ08345Q16832
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4VD (Subject of Investigation/LOI)
Query on 4VD
Download Ideal Coordinates CCD File 
B [auth A]N-[5-({[(3-fluorophenyl)carbamoyl]amino}methyl)-2-methylphenyl]imidazo[1,2-a]pyridine-3-carboxamide
C23 H20 F N5 O2
ZPVUIOVIUFJGHO-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
4VD BindingDB:  7AYM IC50: 3.3 (nM) from 1 assay(s)
EC50: 8.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.75α = 90
b = 85.355β = 90
c = 89.541γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description