9CT8: Tricomplex of Compound 2, KRAS G12D, and CypA

Tricomplex of Compound 2, KRAS G12D, and CypA. Determined by X-ray diffraction at 1.28 Å resolution. Released 23 Jul 2025.

Method: X-ray diffraction
Resolution: 1.28 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,362
Mol. weight: 78.09 kDa
Ligands: GNP, MG, A1AZX
Released: 23 Jul 2025

Explore 9CT8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CT8 contains 18 α-helices and 38 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	1
α-helix	16-25	10
β-strand	37-46	10	1
β-strand	49-58	10	1
α-helix	65-74	10
β-strand	77-83	7	1
α-helix	87-91	5
α-helix	93-104	12
β-strand	111-116	6	1
α-helix	127-137	11
β-strand	141-143	3	1
α-helix	152-168	17

Chain B: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	1-10	10	2
α-helix	16-25	10
β-strand	37-46	10	2
β-strand	49-58	10	2
α-helix	65-74	10
β-strand	77-83	7	2
α-helix	87-91	5
α-helix	93-104	12
β-strand	111-116	6	2
α-helix	127-137	11
β-strand	141-143	3	2
α-helix	152-168	17

Chain C: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	3
β-strand	15-24	10	3
α-helix	30-41	12
β-strand	52	1	3
β-strand	55-57	3	3
β-strand	61-64	4	3
β-strand	77	1	4
β-strand	80	1	4
β-strand	83	1	5
β-strand	97-100	4	3
β-strand	108	1	5
β-strand	112-115	4	3
α-helix	120-122	3
β-strand	128-132	5	3
α-helix	136-144	9
β-strand	156-164	9	3

Chain D: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	6
β-strand	15-24	10	6
α-helix	30-41	12
β-strand	52	1	6
β-strand	55-57	3	6
β-strand	61-64	4	6
β-strand	77	1	7
β-strand	80	1	7
β-strand	83	1	8
β-strand	97-100	4	6
β-strand	108	1	8
β-strand	112-115	4	6
α-helix	120-122	3
β-strand	128-132	5	6
α-helix	136-143	8
β-strand	156-163	8	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2B of GTPase KRas	A, B	protein	170	Homo sapiens	P01116 (AlphaFold model)
Peptidyl-prolyl cis-trans isomerase A	C, D	protein	166	Homo sapiens	P62937 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9CT8_1 Isoform 2B of GTPase KRas (chains A, B)
SMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTA
GQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCD
LPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK

Sequence of entity 2 (C, D), FASTA

>9CT8_2 Peptidyl-prolyl cis-trans isomerase A (chains C, D)
SMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPG
FMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT
EWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE

Ligands and cofactors

ID	Name	Formula	Copies
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2
MG	Magnesium ion	Mg	2
A1AZX	(2R)-2-amino-N-(2-{[(1R)-1-cyclopentyl-2-{[(1M,8S,10S,14S,21M)-22-ethyl-4-hydro…	C51 H68 N8 O8	2

Water and common crystallization additives (CL) are not listed.

Primary citation

A neomorphic protein interface catalyzes covalent inhibition of RAS G12D aspartic acid in tumors. Weller, C., Burnett, G.L., Jiang, L. et al. Science (2025) 389:eads0239-eads0239. DOI 10.1126/science.ads0239 · PubMed

Other PDB entries of the same protein (UniProt P01116 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9IAY 0.95 Å, Structure of 10 in complex with GDP-KRAS
9IAW 1.0 Å, Structure of 5 in complex with GDP-KRAS
12XE 1.01 Å, Crystal structure of KRAS(Q61K) bound to GppNHp and ligand
8ONV 1.01 Å, KRAS-G13D in complex with BI-2493
6P0Z 1.01 Å, Crystal structure of N-acetylated KRAS (2-169) bound to GDP and Mg
9IB5 1.01 Å, Structure of 18 (BI-2493) in complex with GDP-KRAS
8AZZ 1.02 Å, KRAS-G12V in complex with BI-2865
8AZX 1.04 Å, KRAS-G12C in complex with BI-2865
8B00 1.04 Å, KRAS-G13D in complex with BI-2865
8TVK 1.04 Å, KRAS 1-169 G12C Mutant at 100k
4QL3 1.04 Å, Crystal Structure of a GDP-bound G12R Oncogenic Mutant of Human GTPase KRas
8AZV 1.05 Å, KRAS in complex with BI-2865

Browse structure collections

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