7AYM

Structure of DDR2 Kinase domain in complex with IBZ3

• PDB DOI: https://doi.org/10.2210/pdb7AYM/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2020-11-12 Released: 2020-12-16 
• Deposition Author(s): Nawrotek, A., Talagas, A., Vuillard, L.M., Miallau, L.

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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 

Literature

Structure of DDR2 Kinase domain in complex with IBZ3

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 39.05 kDa 
• Atom Count: 2,273 
• Modelled Residue Count: 275 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Discoidin domain-containing receptor 2,Epithelial discoidin domain-containing receptor 1	A	337	Homo sapiens	Mutation(s): 2  Gene Names:  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
UniProt Groups	Q08345Q16832

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4VD (Subject of Investigation/LOI)	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

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 = 41.75	α = 90
b = 85.355	β = 90
c = 89.541	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Nawrotek, A., Talagas, A., Vuillard, L.M., Miallau, L.

Revision History  

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