SMTL ID : 8s8c.1

Structure of Kras in complex with inhibitor MK-1084

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

GDP.1: 21 residues within 4Å: Chain A: A.12, C.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2, 01.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:S.18, A:A.19, A:V.30, A:Y.33, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:S.18, A:D.58 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.18 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.2, H2O.2, H2O.3

1 x 01: (5aSa,17aRa)- 20-Chloro-2-[(2S,5R)-2,5-dimethyl-4-(prop-2-enoyl)piperazin-1-yl]-14,17-difluoro-6-(propan-2-yl)-11,12-dihydro-4H-1,18-(ethanediylidene)pyrido[4,3-e]pyrimido[1,6-g][1,4,7,9]benzodioxadiazacyclododecin-4-one

01.3: 19 residues within 4Å: Chain A: V.10, G.11, A.12, C.13, G.14, K.17, P.35, T.59, A.60, G.61, R.69, M.73, H.96, Y.97, Q.100, I.101, R.103, V.104 Ligands: GDP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.35, A:H.96, A:Y.97, A:Q.100, A:V.104 Hydrogen bonds: A:K.17, A:R.69 pi-Stacking: A:Y.97, A:Y.97 Halogen bonds: A:R.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, X. et al., Discovery of MK-1084: An Orally Bioavailable and Low-Dose KRAS G12C Inhibitor. J.Med.Chem. (2024)

Release Date

2024-07-10

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

Related Entries With Identical Sequence