9L6A | pdb_00009l6a

Crystal structure of KRas G12D (GDP) in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 
    0.245 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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Literature

Discovery of KRAS(G12D) selective degrader ASP3082.

Yoshinari, T.Nagashima, T.Ishioka, H.Inamura, K.Nishizono, Y.Tasaki, M.Iguchi, K.Suzuki, A.Sato, C.Nakayama, A.Amano, Y.Tateishi, Y.Yamanaka, Y.Osaki, F.Yoshino, M.Kuramoto, K.Imaizumi, T.Hayakawa, M.

(2025) Commun Chem 8: 254-254

  • DOI: https://doi.org/10.1038/s42004-025-01662-4
  • Primary Citation of Related Structures:  
    9L6A, 9L6F

  • PubMed Abstract: 

    Kirsten rat sarcoma viral oncogene homolog (KRAS) is one of the most frequently mutated oncogenes in multiple cancers. Multiple types of KRAS mutation are observed in various patients with cancer, and the KRAS(G12D) mutation is the most common. Although multiple covalent inhibitors of the KRAS(G12C) mutation have been identified and clinically validated to date, no drugs have been approved yet for other mutations, including G12D. Herein, we report the discovery and characterization of ASP3082, a KRAS(G12D)-selective degrader, and the crystal structure of the drug-induced ternary complex of KRAS(G12D)/ASP3082/VHL (von Hippel-Lindau). We have also demonstrated an efficient structure-based rational optimization approach, which could be applicable for the optimization of other bifunctional proximity-inducing drugs. ASP3082 effectively induces KRAS(G12D) protein degradation with remarkable selectivity, demonstrates highly efficacious and durable pharmacological activity, and induces tumor regression in multiple KRAS(G12D)-mutated cancer xenograft models. Our results suggest that ASP3082 is a potential therapeutic agent for KRAS(G12D)-mutated cancer, and is now under clinical investigation.


  • Organizational Affiliation
    • Engineered Small Molecules, Astellas Pharma Inc., Tsukuba, Japan. tomohiro.yoshinari@astellas.com.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2B of 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)
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L65 (Subject of Investigation/LOI)
Query on A1L65

Download Ideal Coordinates CCD File 
D [auth A]6-cyclopropyl-4-[(1~{S},4~{S})-2,5-diazabicyclo[2.2.1]heptan-2-yl]-7-(6-fluoranyl-5-methyl-1~{H}-indazol-4-yl)-2-(oxan-4-yloxy)-8-phenylmethoxy-quinazoline
C36 H37 F N6 O3
UVXSJHUAILWCNQ-ZEQRLZLVSA-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:  0.245 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.936α = 90
b = 67.936β = 90
c = 200.1γ = 120
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: 2025-09-03
    Type: Initial release