7V3S

Crystal structure of CMET in complex with a novel inhibitor

PDB DOI: https://doi.org/10.2210/pdb7V3S/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-08-11 Released: 2022-08-17
Deposition Author(s): Su, H.X., Liu, Q.F., Chen, T.T., Li, M.J., Xu, Y.C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.195
R-Value Work: 0.164
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of 10H-Benzo[b]pyrido[2,3-e][1,4]oxazine AXL Inhibitors via Structure-Based Drug Design Targeting c-Met Kinase

Zhan, Z., Ji, Y., Su, H., Fang, C., Peng, X., Liu, Q., Dai, Y., Lin, D., Xu, Y., Ai, J., Duan, W.

(2023) J Med Chem 66: 220-234

DOI: https://doi.org/10.1021/acs.jmedchem.2c00962

Macromolecule Content

Total Structure Weight: 36.55 kDa
Atom Count: 2,530
Modelled Residue Count: 284
Deposited Residue Count: 319
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A	319	Homo sapiens	Mutation(s): 0 Gene Names: MET EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens) Explore P08581 Go to UniProtKB: P08581
PHAROS: P08581 GTEx: ENSG00000105976
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08581
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5I9 (Subject of Investigation/LOI) Query on 5I9 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	~{N}1'-[3-fluoranyl-4-(10~{H}-pyrido[3,2-b][1,4]benzoxazin-4-yloxy)phenyl]-~{N}1-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide C₂₈ H₂₀ F₂ N₄ O₄ ZXKOPASELXTILB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.195
R-Value Work: 0.164
R-Value Observed: 0.166
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.999	α = 90
b = 80.397	β = 90
c = 91.047	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-08-17
Type: Initial release
Version 1.1: 2023-03-08
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.