SMTL ID : 6ark.1

Crystal Structure of compound 10 covalently bound to K-Ras G12C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 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, E.32, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 22 PLIP interactions: 22 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:N.117, A:K.118, A:K.118, A:S.146, A:S.146, A:A.147, A:K.148 Water bridges: A:S.18, A:S.18, A:Y.33, 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: 4 residues within 4Å: Chain A: S.18, Y.33, D.58 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.1, H2O.1, H2O.1

1 x BQD: (3R)-N-(6-bromonaphthalen-2-yl)-3-hydroxy-1-propanoyl-L-prolinamide(Covalent)

BQD.3: 3 residues within 4Å: Chain A: C.13, G.14, N.87 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: N.86, L.121, P.122, S.123, R.124, T.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.86 GOL.5: 3 residues within 4Å: Chain A: Q.151, G.152, D.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.151, A:G.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nnadi, C.I. et al., Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange. J Chem Inf Model (2018)

Release Date

2018-01-31

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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