5T3Q | pdb_00005t3q

Crystal structure of the c-Met kinase domain in complex with a pyrazolone inhibitor

PDB DOI: https://doi.org/10.2210/pdb5T3Q/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2016-08-26 Released: 2016-09-21
Deposition Author(s): Bellon, S.F., Whittington, D.A., Long, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.248 (Depositor), 0.249 (DCC)
R-Value Work:
0.196 (Depositor), 0.197 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Discovery of AMG337: Using structure guided scaffold hydridization to optimize physicochemical properties and target coverage of a MET kinase inhibitor

Boezio, A.A., Peterson, E.A., Harmange, J.-C.

To be published.

Macromolecule Content

Total Structure Weight: 35.77 kDa
Atom Count: 2,472
Modeled Residue Count: 278
Deposited Residue Count: 309
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A	309	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08581
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
75H Query on 75H 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-{3-fluoro-4-[(7-methoxyquinolin-4-yl)oxy]phenyl}-1-(2-hydroxy-2-methylpropyl)-5-methyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazole-4-carboxamide C₃₁ H₂₉ F N₄ O₅ UYMSIPINLJNNOU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
75H	BindingDB: 5T3Q	Ki: 2.7 (nM) from 1 assay(s)
75H	BindingDB: 5T3Q	IC50: min: 2.7, max: 51 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.248 (Depositor), 0.249 (DCC)
R-Value Work: 0.196 (Depositor), 0.197 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.627	α = 90
b = 82.272	β = 90
c = 127.139	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-09-21

Deposition Author(s):

Whittington, D.A.

Revision History (Full details and data files)

Version 1.0: 2016-09-21
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2024-04-03
Changes: Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.