SMTL ID : 9nzm.2 (1 other biounit)

Crystal Structure of Kirsten Rat Sarcoma G12C Complexed with GMPPNP and Covalently Bound to an Adduct of {(2S)-4-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-1-[(2Z)-2-fluoro-3-(pyridin-2-yl)prop-2-enoyl]piperazin-2-yl}acetonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 18 residues within 4Å: Chain A: A.14, C.15, G.16, V.17, G.18, K.19, S.20, A.21, A.62, N.119, K.120, D.122, L.123, S.148, A.149, K.150 Ligands: 01.2, MG.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:A.14, A:G.16, A:V.17, A:G.18, A:K.19, A:K.19, A:S.20, A:A.21, A:N.119, A:K.120, A:K.120, A:A.149, A:K.150 Water bridges: A:S.20 Salt bridges: A:D.122

1 x 01: {(2S)-4-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-1-[(3R)-3-fluoro-3-(pyridin-2-yl)propanoyl]piperazin-2-yl}acetonitrile

01.2: 26 residues within 4Å: Chain A: V.12, G.13, A.14, C.15, G.16, K.19, T.61, A.62, G.63, Q.64, E.65, E.66, Y.67, R.71, D.72, M.75, F.81, K.91, D.95, H.98, Y.99, Q.102, I.103, R.105, V.106 Ligands: GNP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.65, A:Y.67, A:Y.67, A:R.71, A:M.75, A:H.98, A:Q.102, A:I.103, A:V.106, A:V.106 Hydrogen bonds: A:G.13, A:K.19, A:H.98 Salt bridges: A:E.65

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: K.19, S.20, A.62 Ligands: GNP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.20, H2O.1, H2O.2, H2O.3 MG.4: 2 residues within 4Å: Chain A: Q.64, E.65 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Condakes, M.L. et al., Novel covalent warhead imparts potent activity against both GDP- and GTP-bound forms of KRAS G12C. To be published

Release Date

2025-11-05

Peptides

Isoform 2B of GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Isoform 2B of GTPase KRas

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