9E5D

Discovery of an Orally Biovailable KRAS G12D Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.167 

Starting Model: experimental
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Literature

Discovery of INCB159020, an Orally Bioavailable KRAS G12D Inhibitor.

Ye, Q.Shvartsbart, A.Li, Z.Gan, P.Policarpo, R.L.Qi, C.Roach, J.J.Zhu, W.McCammant, M.S.Hu, B.Li, G.Yin, H.Carlsen, P.Hoang, G.Zhao, L.Susick, R.Zhang, F.Lai, C.T.Allali Hassani, A.Epling, L.B.Gallion, A.Kurzeja-Lipinski, K.Gallagher, K.Roman, V.Farren, M.R.Kong, W.Deller, M.C.Zhang, G.Covington, M.Diamond, S.Kim, S.Yao, W.Sokolsky, A.Wang, X.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02662
  • Primary Citation of Related Structures:  
    9E5D, 9E5F

  • PubMed Abstract: 

    The inhibition of mutant KRAS proteins has emerged as a promising approach for treating KRAS-driven cancers, as evidenced by the clinical success of KRAS G12C inhibitors. KRAS G12D, the most common mutant, promises significant expansion of the addressable patient population; however, the reduced nucleophilicity of aspartate compared to cysteine poses significant challenges in balancing sufficient potency with ADME properties to support oral exposure. Herein, we describe the discovery of KRAS G12D inhibitor 23 ( INCB159020 ), which achieves oral exposure in nonhuman primate (NHP). Starting from a weakly potent hit, structure-based drug design was utilized to drive significant potency. Focus on molecular rigidity and balanced polarity then allowed for successful optimization of properties required for oral exposure.


  • Organizational Affiliation

    Department of Discovery Chemistry, Incyte Research Institute, Incyte Corporation, Wilmington, Delaware 19803 United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas170Homo sapiensMutation(s): 1 
Gene Names: KRASKRAS2RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116-2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BEI (Subject of Investigation/LOI)
Query on A1BEI

Download Ideal Coordinates CCD File 
D [auth A]methyl 3-[(7M)-1-[(1R,4R,5S)-2-azabicyclo[2.1.1]hexan-5-yl]-8-(2-cyanoethyl)-4-[3-(dimethylamino)azetidin-1-yl]-6-fluoro-7-(3-hydroxynaphthalen-1-yl)-1H-imidazo[4,5-c]quinolin-2-yl]propanoate
C37 H38 F N7 O3
APCQXEIKSDWIBA-BLLMFBIISA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.04α = 90
b = 53.71β = 90
c = 88.85γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release