9E9I | pdb_00009e9i

Crystal Structure of human KRAS G12C covalently bound to nopinone-derived naphthol compound 21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 
    0.199 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9E9I

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Identification of Structurally Novel KRAS G12C Inhibitors through Covalent DNA-Encoded Library Screening.

Huang, D.Manoni, F.Sun, Z.Liu, R.Allen, J.R.Banerjee, A.Cee, V.J.Eshon, J.Frohn, M.J.Kaller, M.R.Lee, H.Li, C.Li, X.Lopez, P.Ma, V.Medina, J.M.Mohr, C.Mukhina, O.A.Pickrell, A.J.Stellwagen, J.Wu, W.Zhang, W.Zhu, K.Dahal, U.P.Hu, L.A.Leavitt, M.Li, W.Li, Y.Ma, Y.Rex, K.Saiki, A.Y.Wang, P.Sun, Y.Dai, D.Tamayo, N.A.Lanman, B.A.

(2025) J Med Chem 68: 4801-4817

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c03071
  • Primary Citation Related Structures: 
    9E9H, 9E9I

  • PubMed Abstract: 

    Covalent inhibition of the KRAS G12C oncoprotein has emerged as a promising therapeutic approach for the treatment of nonsmall cell lung cancer (NSCLC). The identification of KRAS G12C inhibitors has typically relied on the high-throughput screening (HTS) of libraries of cysteine-reactive small molecules or on the attachment of cysteine-reactive warheads to noncovalent binders of KRAS. Such screening approaches have historically been limited in the size and diversity of molecules that could be effectively screened. DNA-encoded library (DEL) screening has emerged as a promising approach to accelerate the preparation and screening of incredibly large and diverse chemical libraries. Here, we describe the design and synthesis of a covalent DEL to screen ∼16 million compounds against KRAS G12C . We additionally describe the hit identification, validation, and structure-based optimization that culminated in the identification of a series of structurally novel, potent, and selective covalent inhibitors of KRAS G12C with good pharmacokinetic profiles and promising in vivo pharmacodynamic effects.


  • Organizational Affiliation
    • Department of Therapeutic Discovery, Amgen Asia R&D Center, Amgen Research, 4560 Jinke Road, Pudong, Shanghai 201210, P. R. China.

Macromolecule Content 

  • Total Structure Weight: 22.28 kDa 
  • Atom Count: 1,623 
  • Modeled Residue Count: 168 
  • Deposited Residue Count: 184 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2B of GTPase KRas184Homo sapiensMutation(s): 2 
Gene Names: KRASKRAS2RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BH5
(Subject of Investigation/LOI)

Query on A1BH5



Download:Ideal Coordinates CCD File
D [auth A]1-{6-[(4P,6R,8R)-3-fluoro-4-(3-hydroxynaphthalen-1-yl)-7,7-dimethyl-5,6,7,8-tetrahydro-6,8-methanoquinolin-2-yl]-2,6-diazaspiro[3.4]octan-2-yl}propan-1-one
C31 H34 F N3 O2
FKASGFOVUQKHQK-CYFREDJKSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
C [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free:  0.199 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.386α = 90
b = 39.854β = 100.38
c = 52.718γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMACrefinement
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-02-26 
  • Deposition Author(s): Mohr, C.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Database references