SMTL ID : 6zj0.1

CRYSTAL STRUCTURE OF HRAS-G12D IN COMPLEX WITH GCP AND COMPOUND 18

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.17, S.18, T.36 Ligands: GCP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, A:T.36, H2O.1, H2O.1 MG.2: 2 residues within 4Å: Chain A: R.129, Q.130 No protein-ligand interaction detected (PLIP)

1 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.3: 26 residues within 4Å: Chain A: A.12, D.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, D.34, P.35, T.36, A.60, G.61, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.1 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:D.13, A:G.14, A:V.15, A:G.16, A:K.17, A:K.17, A:S.18, A:S.18, A:A.19, A:V.30, A:E.32, A:T.36, A:T.36, A:T.59, A:G.61, A:N.117, A:K.118, A:K.118, A:S.146, A:A.147, A:K.148 Water bridges: A:S.18, A:Y.33, A:D.34 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29

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

EZZ.4: 13 residues within 4Å: Chain A: K.6, L.7, V.8, E.38, S.40, R.42, D.55, I.56, L.57, Q.71, Y.72, T.75, G.76 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.6, A:V.8, A:L.57, A:L.57, A:Q.71, A:Y.72, A:T.75 Hydrogen bonds: A:E.38, A:S.40, A:D.55, A:T.75 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 HRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase HRas