SMTL ID : 6zir.1

CRYSTAL STRUCTURE OF NRAS (C118S) IN COMPLEX WITH GDP AND COMPOUND 18

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: S.18 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.1, H2O.2, H2O.2 MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

GDP.3: 20 residues within 4Å: Chain A: A.12, G.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.1 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:A.147, A:K.148 Water bridges: A:S.18, A:S.18, A:S.18, 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

2 x EZZ: (3~{S})-3-[2-[(dimethylamino)methyl]-1~{H}-indol-3-yl]-5-oxidanyl-2,3-dihydroisoindol-1-one(Non-covalent)

EZZ.4: 7 residues within 4Å: Chain A: Y.5, D.48, G.49, E.50, R.165, Q.166, M.169 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.48, A:R.165 Hydrogen bonds: A:Y.5, A:D.48, A:E.50 pi-Cation interactions: A:R.165, A:R.165 EZZ.5: 12 residues within 4Å: Chain A: K.6, L.7, V.8, E.38, S.40, R.42, D.55, L.57, Q.71, Y.72, T.75, G.76 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.6, A:V.8, A:L.57, A:L.57, A:Y.72, A:T.75 Hydrogen bonds: A:D.55, A:T.75 Water bridges: A:R.42 Salt bridges: A:D.55 pi-Cation interactions: A:K.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kessler, D. et al., Drugging all RAS isoforms with one pocket. Future Med Chem (2020)

Release Date

2020-08-19

Peptides

GTPase NRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase NRas

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