8OUU | pdb_00008ouu

Crystal structure of D1228V c-MET bound by compound 29

PDB DOI: https://doi.org/10.2210/pdb8OUU/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-04-24 Released: 2023-07-05
Deposition Author(s): Collie, G.W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.225 (Depositor), 0.220 (DCC)
R-Value Work:
0.202 (Depositor), 0.196 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery and Optimization of the First ATP Competitive Type-III c-MET Inhibitor.

Michaelides, I.N., Collie, G.W., Borjesson, U., Vasalou, C., Alkhatib, O., Barlind, L., Cheung, T., Dale, I.L., Embrey, K.J., Hennessy, E.J., Khurana, P., Koh, C.M., Lamb, M.L., Liu, J., Moss, T.A., O'Neill, D.J., Phillips, C., Shaw, J., Snijder, A., Storer, R.I., Stubbs, C.J., Han, F., Li, C., Qiao, J., Sun, D.Q., Wang, J., Wang, P., Yang, W.

(2023) J Med Chem 66: 8782-8807

PubMed: 37343272 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.3c00401
Primary Citation Related Structures:
8OUU, 8OUV, 8OV7, 8OVZ, 8OW3, 8OWG

PubMed Abstract:
Recent clinical reports have highlighted the need for wild-type (WT) and mutant dual inhibitors of c-MET kinase for the treatment of cancer. We report herein a novel chemical series of ATP competitive type-III inhibitors of WT and D1228V mutant c-MET. Using a combination of structure-based drug design and computational analyses, ligand 2 was optimized to a highly selective chemical series with nanomolar activities in biochemical and cellular settings. Representatives of the series demonstrate excellent pharmacokinetic profiles in rat in vivo studies with promising free-brain exposures, paving the way for the design of brain permeable drugs for the treatment of c-MET driven cancers.

Organizational Affiliation

Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom.

Macromolecule Content

Total Structure Weight: 70.82 kDa
Atom Count: 5,064
Modeled Residue Count: 574
Deposited Residue Count: 618
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	309	Homo sapiens	Mutation(s): 1 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W49 (Subject of Investigation/LOI) Query on W49 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	5-(3-ethynyl-5-fluoranyl-1H-indazol-7-yl)-1-[(1S)-1-phenylethyl]pyrimidine-2,4-dione C₂₁ H₁₅ F N₄ O₂ XZWWEKACMFDCHL-LBPRGKRZSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B], H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	E [auth A], I [auth B], J [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
W49	BindingDB: 8OUU	IC50: min: 13, max: 20 (nM) from 2 assay(s)
W49	BindingDB: 8OUU	EC50: min: 339, max: 1170 (nM) from 2 assay(s)