12FF | pdb_000012ff

KRAS G12V in complex with GDP and a macrocyclic inhibitor (Compound 20).

PDB DOI: https://doi.org/10.2210/pdb12FF/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2026-04-01 Released: 2026-09-09
Deposition Author(s): DiDonato, M., Spraggon, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.274 (Depositor), 0.278 (DCC)
R-Value Work:
0.241 (Depositor), 0.248 (DCC)
R-Value Observed:
0.242 (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

Lead Optimization of Multimutant KRAS Switch-II Pocket Macrocyclic Inhibitors via Isosteric Replacement to Improve ADME and Oral Exposure

Phillips, D.P., Alper, P.B., Borkin, D., Han, D., Kochanek, S.E., Gurjar, J., Mathison, C.J.N., Nelson, J.M., Pei, W., Nguyen, B.N., Hoffman, T., Okram, B., Nguyen, T.N., Jiang, S., Masick, B.T., Wang, Z., Cho, C.Y., Yin, H., Chen, Y., Juarez, J., Jia, Y., Zhou, V., Liu, G., Wright, C., Nguyen, T., Knee, D.A., Liu, Q., Liu, J., Li, J., Virata, C., de Oliveira, C., DiDonato, M., Bursulaya, B., Vidal-Biggart, A., Jones, D.H., Witmer, D., Chu, C., Jin, H., Herath, A., Richmond, W., Groessl, T., Shapiro, M., Effenberger, K., Arroyo, K., Bretz, A., Honda, A., Gordon, W.P., Molteni, V., Haling, J.R.

(2026) J Med Chem

DOI: https://doi.org/10.1021/acs.jmedchem.6c01454

Macromolecule Content

Total Structure Weight: 82.42 kDa
Atom Count: 6,091
Modeled Residue Count: 672
Deposited Residue Count: 684
Unique protein chains: 1

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	171	Homo sapiens	Mutation(s): 4 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1DB0( Subject of Investigation/LOI) Query on A1DB0 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	F [auth A], K [auth B], P [auth C], T [auth D]	(5S,9R,21bP)-25-fluoro-3-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}-9-methyl-7,8,9,10,14,15,16,19-octahydro-13H-5,9-methano-22,1-(metheno)pyrimido[4',5':9,10][1,3,8]oxadiazacyclononadecino[14,15-e]indazol-11(6H)-one C₃₄ H₃₉ F₂ N₇ O₃ UGFJXOPXCUKURZ-NMUJKEQYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain U [auth D] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C]	G [auth A], L [auth B], Q [auth C], U [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D]	H [auth A] I [auth A] M [auth B] N [auth B] R [auth C] H [auth A], I [auth A], M [auth B], N [auth B], R [auth C], V [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D]	E [auth A], J [auth B], O [auth C], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain S [auth D]