SMTL ID : 6n2k.1

Tetrahydropyridopyrimidines as Covalent Inhibitors of KRAS-G12C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 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, K9J.3 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.12, A:G.14, A:V.15, A:G.16, A:K.17, A:S.18, A:A.19, A:V.30, A:N.117, A:K.118, A:K.118, A:S.146, A:A.147, A:K.148 Water bridges: A:S.18, A:S.18, A:D.31, A:D.31, A:Y.33 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.3, H2O.4

1 x K9J: 1-{4-[2-{[(2R)-1-(dimethylamino)propan-2-yl]oxy}-7-(3-hydroxynaphthalen-1-yl)-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]piperazin-1-yl}propan-1-one(Covalent)

K9J.3: 24 residues within 4Å: Chain A: G.11, A.12, C.13, K.17, P.35, T.59, A.60, G.61, E.63, E.64, Y.65, S.66, R.69, D.70, M.73, K.89, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 Ligands: GDP.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.12, A:P.35, A:E.63, A:Y.65, A:R.69, A:M.73, A:Y.97, A:Y.97, A:Q.100, A:I.101, A:V.104 Hydrogen bonds: A:K.17, A:E.64, A:D.70, A:Y.97 Water bridges: A:Y.65 Salt bridges: A:E.63, A:D.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fell, J.B. et al., Discovery of Tetrahydropyridopyrimidines as Irreversible Covalent Inhibitors of KRAS-G12C with In Vivo Activity. ACS Med Chem Lett (2018)

Release Date

2018-12-12

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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