SMTL ID : 7tle.1

Crystal Structure of small molecule beta-lactone 1 covalently bound to K-Ras(G12S)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: S.17 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.17, H2O.1, H2O.1, H2O.2, H2O.2

1 x I6T: (3R,4R)-1-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-3-hydroxypiperidine-4-carbaldehyde(Covalent)

I6T.2: 20 residues within 4Å: Chain A: V.9, G.10, A.11, S.12, K.16, A.59, G.60, E.62, E.63, Y.64, R.68, D.69, M.72, D.92, H.95, Y.96, Q.99, I.100, R.102, V.103 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:E.62, A:Y.64, A:M.72, A:H.95, A:Q.99, A:I.100, A:V.103, A:V.103 Hydrogen bonds: A:G.10, A:K.16, A:E.62, A:Y.96 Water bridges: A:G.10, A:G.60 Salt bridges: A:E.62, A:D.92

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

GDP.3: 20 residues within 4Å: Chain A: A.11, S.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, Y.32, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.1 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.11, A:G.13, A:V.14, A:G.15, A:K.16, A:S.17, A:A.18, A:V.29, A:N.116, A:K.117, A:K.117, A:S.145, A:A.146, A:K.147 Water bridges: A:S.17, A:S.17, A:Y.32 Salt bridges: A:K.16, A:D.119 pi-Stacking: A:F.28, A:F.28

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: H.27, F.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.28 Salt bridges: A:H.27

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