24HR | pdb_000024hr

Human KRAS G12D (GDP-bound) in complex with macrocyclic peptide inhibitor AP6252

PDB DOI: https://doi.org/10.2210/pdb24HR/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2026-03-04 Released: 2026-05-27
Deposition Author(s): Yamano, T., Chiyoda, A., Fukami, T.A., Tanada, M., Irie, M., Torizawa, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.270 (Depositor), 0.272 (DCC)
R-Value Work:
0.228 (Depositor), 0.229 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure-Activity Relationship Analysis of Macrocyclic Peptide RAS Inhibitors: Spotlight on the Solvent-Exposed Region.

Chiyoda, A., Matsuo, A., Yamano, T., Tanada, M.

(2026) ACS Med Chem Lett 17: 1310-1315

PubMed: 42305191 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.6c00122
Primary Citation Related Structures:
24HR, 24HS, 24HT

PubMed Abstract:
As ligand molecular weight increases, strategic structural optimization becomes increasingly important because larger ligands contain more modifiable atoms, making comprehensive exploration impractical. We present the structure-activity relationship (SAR) analysis of LUNA18 (paluratide, an 11-mer macrocyclic peptide RAS inhibitor) focusing on the amino acid side chains at position 5 in the solvent-exposed region. The analysis revealed that the contribution of position 5 to inhibitory activity depends on its local environment. Structural analysis identified two structural features: peptides forming a ″cavity″, which possess the hydrophobic interaction network among positions 1, 8, and 9, exhibited minimal changes upon position 5 modification, whereas those forming a ″groove″, lacking this interaction network, showed significant differences. These findings provide practical guidelines for optimizing macrocyclic peptides: evaluate the contributions of solvent-exposed side chain at key points and interpret SARs in the context of spatially proximal side chains.

Organizational Affiliation

Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan.

Macromolecule Content

Total Structure Weight: 90.11 kDa
Atom Count: 6,254
Modeled Residue Count: 742
Deposited Residue Count: 764
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2B of GTPase KRas	A, B, C, D	179	Homo sapiens	Mutation(s): 1 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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AP6252	E [auth I], F [auth J], G [auth K], H [auth L]	12	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain I [auth A] SDF format, chain RA [auth C] SDF format, chain XA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain XA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain XA [auth D]	AA [auth B], I [auth A], RA [auth C], XA [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain AA [auth B] Focus chain I [auth A] Focus chain RA [auth C] Focus chain XA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain I [auth A] Focus chain RA [auth C] Focus chain XA [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain BB [auth I] SDF format, chain FA [auth B] SDF format, chain HA [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain N [auth A] SDF format, chain S [auth A] SDF format, chain V [auth A] SDF format, chain YA [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth I] MOL2 format, chain FA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain S [auth A] MOL2 format, chain V [auth A] MOL2 format, chain YA [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth I] mmCIF format, chain FA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain S [auth A] mmCIF format, chain V [auth A] mmCIF format, chain YA [auth D]	BA [auth B] BB [auth I] FA [auth B] HA [auth B] J [auth A] BA [auth B], BB [auth I], FA [auth B], HA [auth B], J [auth A], K [auth A], L [auth A], LA [auth B], N [auth A], S [auth A], V [auth A], YA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain BB [auth I] Focus chain FA [auth B] Focus chain HA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth B] Focus chain N [auth A] Focus chain S [auth A] Focus chain V [auth A] Focus chain YA [auth D] Interactions & Density Focus chain BA [auth B] Focus chain BB [auth I] Focus chain FA [auth B] Focus chain HA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth B] Focus chain N [auth A] Focus chain S [auth A] Focus chain V [auth A] Focus chain YA [auth D]
FMT (Subject of Investigation/LOI) Query on FMT Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain GA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain SA [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain W [auth A] SDF format, chain X [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A]	CA [auth B] DA [auth B] EA [auth B] GA [auth B] IA [auth B] CA [auth B], DA [auth B], EA [auth B], GA [auth B], IA [auth B], JA [auth B], KA [auth B], M [auth A], MA [auth B], NA [auth B], O [auth A], P [auth A], Q [auth A], QA [auth C], R [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], W [auth A], X [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain W [auth A] Focus chain X [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth D] mmCIF format, chain AB [auth D] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth D]	AB [auth D] OA [auth B] PA [auth B] VA [auth C] WA [auth C] AB [auth D], OA [auth B], PA [auth B], VA [auth C], WA [auth C], Y [auth A], Z [auth A], ZA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain Y [auth A] Focus chain Z [auth A] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain Y [auth A] Focus chain Z [auth A] Focus chain ZA [auth D]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
7T2 Query on 7T2	E [auth I], F [auth J], G [auth K], H [auth L]	L-PEPTIDE LINKING	C₁₀ H₁₂ Cl N O₂		PHE
A1MFG Query on A1MFG	E [auth I], F [auth J], G [auth K], H [auth L]	L-PEPTIDE LINKING	C₁₁ H₁₁ F₄ N O₂		--
AC5 Query on AC5	E [auth I], F [auth J], G [auth K], H [auth L]	PEPTIDE LINKING	C₆ H₁₁ N O₂		--
MLE Query on MLE	E [auth I], F [auth J], G [auth K], H [auth L]	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU
SAR Query on SAR	E [auth I], F [auth J], G [auth K], H [auth L]	PEPTIDE LINKING	C₃ H₇ N O₂		GLY