5HTI | pdb_00005hti

Crystal structure of c-Met kinase domain in complex with LXM108

• PDB DOI: https://doi.org/10.2210/pdb5HTI/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-01-26 Released: 2017-02-01 
• Deposition Author(s): Liu, Q.F., Xu, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of c-Met kinase domain in complex with LXM108

Xu, Y.C., Long, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.62 kDa 
• Atom Count: 2,571 
• Modeled Residue Count: 290 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
66L	B [auth A]	N-[3-fluoro-4-({7-[2-(morpholin-4-yl)ethoxy]-1,6-naphthyridin-4-yl}oxy)phenyl]-N'-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide C31 H29 F2 N5 O5 GGMOWJSRHCAARI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.894	α = 90
b = 80.557	β = 90
c = 91.449	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	data scaling
HKL-3000	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Liu, Q.F., Xu, Y.C.

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description