3F66 | pdb_00003f66

Human c-Met Kinase in complex with quinoxaline inhibitor

PDB DOI: https://doi.org/10.2210/pdb3F66/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2008-11-05 Released: 2008-12-23
Deposition Author(s): Meier, C., Ceska, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.225 (Depositor), 0.231 (DCC)
R-Value Work:
0.168 (Depositor), 0.177 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of a novel series of quinoxalines as inhibitors of c-Met kinase.

Porter, J., Lumb, S., Lecomte, F., Reuberson, J., Foley, A., Calmiano, M., le Riche, K., Edwards, H., Delgado, J., Franklin, R.J., Gascon-Simorte, J.M., Maloney, A., Meier, C., Batchelor, M.

(2009) Bioorg Med Chem Lett 19: 397-400

PubMed: 19059779 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.11.062
Primary Citation Related Structures:
3F66

PubMed Abstract:
A series of quinoxaline inhibitors of c-Met kinase is described. The postulated binding mode was confirmed by an X-ray crystal structure and optimisation of the series was performed on the basis of this structure. Future directions for development of the series are discussed together with the identification of a novel quinoline scaffold.

Organizational Affiliation

UCB Celltech, 216 Bath Road, Slough SL1 3WE, United Kingdom. john.porter@ucb-group.com

Macromolecule Content

Total Structure Weight: 68.92 kDa
Atom Count: 5,160
Modeled Residue Count: 557
Deposited Residue Count: 596
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A, B	298	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IHX Query on IHX Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	3-[3-(4-methylpiperazin-1-yl)-7-(trifluoromethyl)quinoxalin-5-yl]phenol C₂₀ H₁₉ F₃ N₄ O QNCYYRHIUFGGJX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GBL Query on GBL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	GAMMA-BUTYROLACTONE C₄ H₆ O₂ YEJRWHAVMIAJKC-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
IHX	BindingDB: 3F66	IC50: 900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.225 (Depositor), 0.231 (DCC)
R-Value Work: 0.168 (Depositor), 0.177 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.377	α = 100.7
b = 47.587	β = 103.62
c = 75.6	γ = 98.29

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-12-23

Deposition Author(s):

Meier, C.

Ceska, T.

Revision History (Full details and data files)

Version 1.0: 2008-12-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Derived calculations