8VI1 | pdb_00008vi1

Crystal structure of c-Met-D1228N in complex with KIN-7615


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 
    0.298 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.251 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 
    0.253 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of KIN-8741, a Highly Selective Type IIb c-Met Kinase Inhibitor with Broad Mutation Coverage and Quality Drug-Like Properties for the Treatment of Cancer.

Ouyang, X.S.Grandinetti, K.B.Boren, M.Chakravorty, S.Chopade, S.Jiang, P.Kanouni, T.Koudriakova, T.Makwana, O.Pack, S.K.Perez, M.Suriben, R.Timple, N.Thohan, S.Uryu, S.Womble, S.Yuan, D.Kania, R.S.Cox, J.M.

(2025) J Med Chem 68: 10648-10662

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00834
  • Primary Citation Related Structures: 
    8VI1

  • PubMed Abstract: 

    Mesenchymal-epithelial transition factor (c-Met) is a receptor tyrosine kinase belonging to the MET gene family. Aberrant c-Met signaling drives tumorigenesis. Acquired drug resistance to current type I c-Met inhibitors has limited their duration of response. Many type II inhibitors have been developed to address the on-target resistance mutations that render type I inhibitors ineffective. However, type II inhibitors, to date, have not been approved to treat c-Met-driven cancers due to poor selectivity and suboptimal physicochemical properties that limit free drug concentrations. Herein, we describe how structure-based drug design (SBDD) directed at optimization of lipophilic efficiency (LipE) enabled the discovery of a highly selective type IIb c-Met inhibitor with quality drug-like properties. Lead compound KIN-8741 exhibits broad potency against acquired resistance mutations and a desirable safety profile that supported the filing and clearance of an IND for the treatment of cancer.


  • Organizational Affiliation
    • Kinnate Biopharma Inc., San Diego, California 92130, United States.

Macromolecule Content 

  • Total Structure Weight: 70.68 kDa 
  • Atom Count: 4,617 
  • Modeled Residue Count: 571 
  • Deposited Residue Count: 618 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor
A, B
309Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08581
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AB1
(Subject of Investigation/LOI)

Query on A1AB1



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
N-(3,5-difluoro-4-{[6-(2-hydroxyethoxy)-7-methoxyquinolin-4-yl]oxy}phenyl)-4-methoxypyridine-3-carboxamide
C25 H21 F2 N3 O6
RKCHWRYEFHSLOC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free:  0.298 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.251 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 0.253 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.66α = 90
b = 69.82β = 95.84
c = 78.06γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Database references
  • Version 1.2: 2025-06-25
    Changes: Database references