9L6F | pdb_00009l6f

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

PDB DOI: https://doi.org/10.2210/pdb9L6F/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-12-24 Released: 2025-09-03
Deposition Author(s): Amano, Y., Tateishi, Y.
Funding Organization(s): Not funded

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
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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

PubMed: 40849515 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42004-025-01662-4
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 255.21 kDa
Atom Count: 16,509
Modeled Residue Count: 2,016
Deposited Residue Count: 2,188
Unique protein chains: 4

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	A, E, I, M	163	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40337
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	B, F, J, N	96	Homo sapiens	Mutation(s): 0 Gene Names: ELOC, TCEB1
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15369
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	C, G, K, O	118	Homo sapiens	Mutation(s): 0 Gene Names: ELOB, TCEB2
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15370
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2B of GTPase KRas	D, H, L, P	170	Homo sapiens	Mutation(s): 1 Gene Names: KRAS, KRAS2, RASK2 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01116
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L66 (Subject of Investigation/LOI) Query on A1L66 Download:Ideal Coordinates CCD File SDF format, chain BA [auth P] SDF format, chain Q [auth A] SDF format, chain V [auth H] SDF format, chain Y [auth L] MOL2 format, chain BA [auth P] MOL2 format, chain Q [auth A] MOL2 format, chain V [auth H] MOL2 format, chain Y [auth L] mmCIF format, chain BA [auth P] mmCIF format, chain Q [auth A] mmCIF format, chain V [auth H] mmCIF format, chain Y [auth L]	BA [auth P], Q [auth A], V [auth H], Y [auth L]	ASP3082 C₆₀ H₆₅ F N₁₂ O₇ S XXWMEQMGQNHRAF-WFJRNIGCSA-N		Interactions Focus chain BA [auth P] Focus chain Q [auth A] Focus chain V [auth H] Focus chain Y [auth L] Interactions & Density Focus chain BA [auth P] Focus chain Q [auth A] Focus chain V [auth H] Focus chain Y [auth L]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain T [auth H] SDF format, chain W [auth L] SDF format, chain Z [auth P] MOL2 format, chain R [auth D] MOL2 format, chain T [auth H] MOL2 format, chain W [auth L] MOL2 format, chain Z [auth P] mmCIF format, chain R [auth D] mmCIF format, chain T [auth H] mmCIF format, chain W [auth L] mmCIF format, chain Z [auth P]	R [auth D], T [auth H], W [auth L], Z [auth P]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain R [auth D] Focus chain T [auth H] Focus chain W [auth L] Focus chain Z [auth P] Interactions & Density Focus chain R [auth D] Focus chain T [auth H] Focus chain W [auth L] Focus chain Z [auth P]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth P] SDF format, chain S [auth D] SDF format, chain U [auth H] SDF format, chain X [auth L] MOL2 format, chain AA [auth P] MOL2 format, chain S [auth D] MOL2 format, chain U [auth H] MOL2 format, chain X [auth L] mmCIF format, chain AA [auth P] mmCIF format, chain S [auth D] mmCIF format, chain U [auth H] mmCIF format, chain X [auth L]	AA [auth P], S [auth D], U [auth H], X [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth P] Focus chain S [auth D] Focus chain U [auth H] Focus chain X [auth L] Interactions & Density Focus chain AA [auth P] Focus chain S [auth D] Focus chain U [auth H] Focus chain X [auth L]