7AYM | pdb_00007aym

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.289 (Depositor), 0.310 (DCC)
R-Value Work:
0.236 (Depositor), 0.250 (DCC)
R-Value Observed:
0.239 (Depositor)

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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... 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16832
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4VD (Subject of Investigation/LOI) Query on 4VD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
4VD	BindingDB: 7AYM	IC50: 3.3 (nM) from 1 assay(s)
4VD	BindingDB: 7AYM	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 (Depositor), 0.310 (DCC)
R-Value Work: 0.236 (Depositor), 0.250 (DCC)
R-Value Observed: 0.239 (Depositor)

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-12-16

Deposition Author(s):

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.