SMTL ID : 7tlg.1 (1 other biounit)

Crystal Structure of small molecule beta-lactone 5 covalently bound to K-Ras(G12S)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

GDP.1: 19 residues within 4Å: Chain A: A.12, S.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.3 19 PLIP interactions: 19 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:D.31, A:N.117, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:S.18, A:S.18, A:D.31, A:K.148 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29

1 x I7H: (3R,4R)-1-[7-(8-chloronaphthalen-1-yl)-8-fluoro-2-{[(4S,7as)-tetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-4-yl]-3-hydroxypiperidine-4-carbaldehyde(Covalent)

I7H.2: 24 residues within 4Å: Chain A: V.10, G.11, A.12, S.13, K.17, T.59, A.60, G.61, Q.62, E.63, E.64, Y.65, R.69, D.70, M.73, F.79, K.89, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.65, A:R.69, A:M.73, A:Q.100, A:I.101, A:V.104, A:V.104 Hydrogen bonds: A:K.17, A:K.17, A:R.69 Water bridges: A:G.11, A:G.61, A:Y.65, A:Y.97 Salt bridges: A:E.63

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 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.2, H2O.2, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Chemical acylation of an acquired serine suppresses oncogenic signaling of K-Ras(G12S). Nat.Chem.Biol. (2022)

Release Date

2022-08-03

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

Related Entries With Identical Sequence