SMTL ID : 9nzn.1

Crystal Structure of Kirsten Rat Sarcoma G12C Complexed with GDP and Covalently Bound to an Adduct of (2S)-1-{4-[(7P)-7-(8-ethynyl-7-fluoro-3-hydroxynaphthalen-1-yl)-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-4-yl]piperazin-1-yl}-2-fluoro-3-(1,3-thiazol-2-yl)propan-1-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 23 residues within 4Å: Chain A: A.14, C.15, G.16, V.17, G.18, K.19, S.20, A.21, F.31, V.32, D.33, E.34, Y.35, P.37, N.119, K.120, D.122, L.123, S.148, A.149, K.150 Ligands: 01.2, MG.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.16, A:V.17, A:G.18, A:K.19, A:S.20, A:A.21, A:D.33, A:D.33, A:Y.35, A:N.119, A:K.120, A:K.120, A:A.149, A:K.150 Water bridges: A:S.20, A:S.20, A:D.33 Salt bridges: A:K.19, A:D.122 pi-Stacking: A:F.31, A:F.31

1 x 01: (2S)-1-{4-[(7P)-7-(8-ethynyl-7-fluoro-3-hydroxynaphthalen-1-yl)-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-4-yl]piperazin-1-yl}-2-fluoro-3-(1,3-thiazol-2-yl)propan-1-one

01.2: 28 residues within 4Å: Chain A: V.12, G.13, A.14, C.15, K.19, P.37, T.38, T.61, A.62, G.63, Q.64, E.65, E.66, Y.67, S.68, 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: GDP.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.12, A:P.37, A:E.65, A:Y.67, A:R.71, A:M.75, A:Y.99, A:Y.99, A:Q.102, A:I.103 Hydrogen bonds: A:K.19, A:G.63, A:Y.67, A:R.71, A:R.71, A:D.72, A:D.72, A:H.98, A:Y.99, A:R.105 Salt bridges: A:E.65

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: K.19, S.20, Y.35, P.37, A.62 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.20, H2O.1, H2O.1, H2O.1, H2O.3

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
A

Isoform 2B of GTPase KRas

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