24SS | pdb_000024ss

Human KRAS WT (GDP-bound) in complex with macrocyclic peptide inhibitor AUBE00

PDB DOI: https://doi.org/10.2210/pdb24SS/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-03-19 Released: 2026-09-16
Deposition Author(s): Yamano, T., Kage, M., Fukami, T.A., Tanada, M., Irie, M., Torizawa, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.177 (Depositor), 0.177 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: 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

Exploiting Bridged Conformations for Precise Molecular Recognition in the Design of KRAS-Selective, Orally Available Macrocyclic Peptides

Kage, M., Kawada, H., Takano, K., Matsuo, A., Murata, Y., Hashimoto, S., Tamiya, M., Kotake, T., Kuramoto, S., Yamano, T., Irie, M., Ohara, K., Sakurai, Y., Nomura, K., Morita, Y., Hayashi, R., Wakamiya, Y., Takei, K., Tanaka, H., Nishimura, Y., Iikura, H., Shiraishi, T., Tanada, M.

(2026) J Am Chem Soc

DOI: https://doi.org/10.1021/jacs.6c14212

Macromolecule Content

Total Structure Weight: 68.74 kDa
Atom Count: 5,351
Modeled Residue Count: 560
Deposited Residue Count: 573
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	179	Homo sapiens	Mutation(s): 0 Gene Names: KRAS, KRAS2, RASK2 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01116-2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AUBE00	D [auth I], E [auth J], F [auth K]	12	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 G [auth A] SDF format, chain KA [auth C] SDF format, chain V [auth B] MOL2 format, chain G [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain V [auth B] mmCIF format, chain G [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain V [auth B]	G [auth A], KA [auth C], V [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain KA [auth C] Focus chain V [auth B] Interactions & Density Focus chain G [auth A] Focus chain KA [auth C] Focus chain V [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain TA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C]	T [auth A], TA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain T [auth A] Focus chain TA [auth C] Interactions & Density Focus chain T [auth A] Focus chain TA [auth C]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain UA [auth C] MOL2 format, chain UA [auth C] mmCIF format, chain UA [auth C]	UA [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain UA [auth C] Interactions & Density Focus chain UA [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain S [auth A] SDF format, chain U [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain U [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain U [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], H [auth A], I [auth A], IA [auth B], J [auth A], JA [auth C], K [auth A], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], QA [auth C], R [auth A], RA [auth C], S [auth A], U [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain U [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain U [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain Q [auth A] SDF format, chain SA [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain SA [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain SA [auth C]	HA [auth B], Q [auth A], SA [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain Q [auth A] Focus chain SA [auth C] Interactions & Density Focus chain HA [auth B] Focus chain Q [auth A] Focus chain SA [auth C]

Modified Residues 8 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
7VN Query on 7VN	D [auth I], E [auth J], F [auth K]	L-PEPTIDE LINKING	C₈ H₁₅ N O₂		ALA
A1L7N Query on A1L7N	D [auth I], E [auth J], F [auth K]	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		--
A1MFO Query on A1MFO	D [auth I], E [auth J], F [auth K]	L-PEPTIDE LINKING	C₁₄ H₁₆ F₃ N O₂		--
A1MFP Query on A1MFP	D [auth I], E [auth J], F [auth K]	L-PEPTIDE LINKING	C₆ H₁₁ N O₂		--
A1MFQ Query on A1MFQ	D [auth I], E [auth J], F [auth K]	L-PEPTIDE LINKING	C₁₂ H₁₄ F₃ N O₃		--
A1MFR Query on A1MFR	D [auth I], E [auth J], F [auth K]	PEPTIDE LINKING	C₆ H₁₁ N O₂		--
SAR Query on SAR	D [auth I], E [auth J], F [auth K]	PEPTIDE LINKING	C₃ H₇ N O₂		GLY
ZNY Query on ZNY	D [auth I], E [auth J], F [auth K]	L-PEPTIDE LINKING	C₇ H₁₃ N O₃		--