SMTL ID : 8cx5.2 (1 other biounit)

Crystal Structure of small molecule alpha,beta-ketoamide 4 covalently bound to K-Ras(G12R)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.18, D.58 Ligands: GDP.5 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.1, H2O.2, H2O.3

1 x P7U: {(2S)-4-[(7P)-7-(8-chloronaphthalen-1-yl)-8-fluoro-2-{[(4R,7as)-tetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-4-yl]-1-[(3S)-2,2,3-trihydroxybutanoyl]piperazin-2-yl}acetonitrile(Covalent)

P7U.2: 20 residues within 4Å: Chain A: V.10, G.11, R.13, K.17, T.59, A.60, G.61, E.63, E.64, Y.65, D.70, M.73, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 Ligands: PO4.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.13, A:E.63, A:Y.65, A:Y.65, A:M.73, A:Q.100, A:I.101 Hydrogen bonds: A:G.11, A:G.61 Water bridges: A:Y.97 Salt bridges: A:E.63

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 2 residues within 4Å: Chain A: Y.41, R.42 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.42, A:R.42, A:R.42 Salt bridges: A:R.42 PO4.4: 4 residues within 4Å: Chain A: A.12, R.13, D.93 Ligands: P7U.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.13, A:D.93 Water bridges: A:Y.97, A:Y.97

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

GDP.5: 19 residues within 4Å: Chain A: A.12, R.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, D.31, E.32, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.1 21 PLIP interactions: 21 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:D.31, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:K.17, A:S.18, A:S.18, A:Y.33 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 2 residues within 4Å: Chain A: P.122, S.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.123, A:S.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Chemoselective Covalent Modification of K-Ras(G12R) with a Small Molecule Electrophile. J.Am.Chem.Soc. (2022)

Release Date

2022-08-31

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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