9L6F | pdb_00009l6f

Crystal structure of KRas G12D (GDP) in complex with ASP3082


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 
    0.305 (Depositor), 0.308 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


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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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressor
A, E, I, M
163Homo sapiensMutation(s): 0 
Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens)
Explore P40337 
Go to UniProtKB:  P40337
PHAROS:  P40337
GTEx:  ENSG00000134086 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40337
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-C
B, F, J, N
96Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
PHAROS:  Q15369
GTEx:  ENSG00000154582 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15369
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-B
C, G, K, O
118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
PHAROS:  Q15370
GTEx:  ENSG00000103363 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15370
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2B of GTPase KRas
D, H, L, P
170Homo 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  
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UniProt GroupP01116
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L66 (Subject of Investigation/LOI)
Query on A1L66

Download Ideal Coordinates CCD File 
BA [auth P],
Q [auth A],
V [auth H],
Y [auth L]
ASP3082
C60 H65 F N12 O7 S
XXWMEQMGQNHRAF-WFJRNIGCSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
R [auth D],
T [auth H],
W [auth L],
Z [auth P]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth P],
S [auth D],
U [auth H],
X [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free:  0.305 (Depositor), 0.308 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.348α = 90
b = 58.905β = 104.3
c = 165.979γ = 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: 2025-09-03
    Type: Initial release