SMTL ID : 7ach.1

CRYSTAL STRUCTURE OF ACTIVE KRAS G12D (GPPCP) IN COMPLEX WITH THE SOAKED DIMERIC INHIBITOR BI-5747

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

1 x R6W: (3~{S})-5-oxidanyl-3-[2-[[6-[[3-[(1~{S})-6-oxidanyl-3-oxidanylidene-1,2-dihydroisoindol-1-yl]-1~{H}-indol-2-yl]methylamino]hexylamino]methyl]-1~{H}-indol-3-yl]-2,3-dihydroisoindol-1-one(Non-covalent)

R6W.1: 22 residues within 4Å: Chain A: K.6, L.7, V.8, E.38, S.40, D.55, L.57, Q.71, Y.72, T.75, G.76 Chain B: K.6, L.7, V.8, E.38, S.40, D.55, L.57, Q.71, Y.72, T.75, G.76 21 PLIP interactions: 12 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:K.6, B:V.8, B:L.57, B:L.57, B:Q.71, B:Y.72, A:K.6, A:V.8, A:L.57, A:Q.71, A:Y.72 Hydrogen bonds: B:E.38, B:S.40, B:S.40, B:D.55, A:D.55, A:T.75 pi-Cation interactions: B:K.6, B:K.6, A:K.6 Water bridges: A:S.40

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

GCP.2: 24 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, P.35, T.36, G.61, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.3 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:K.17, A:S.18, A:A.19, A:V.30, A:T.36, A:T.36, A:G.61, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:S.18, A:T.36, A:Q.62, A:Q.62 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29 GCP.4: 24 residues within 4Å: Chain B: 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, P.35, T.36, G.61, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.5 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.14, B:V.15, B:G.16, B:K.17, B:K.17, B:S.18, B:A.19, B:V.30, B:Y.33, B:T.36, B:G.61, B:N.117, B:K.118, B:K.118, B:A.147, B:K.148 Water bridges: B:S.18, B:D.34, B:Q.62, B:Q.62, B:K.148 Salt bridges: B:D.120 pi-Stacking: B:F.29, B:F.29

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: S.18, T.36 Ligands: GCP.2 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.5: 3 residues within 4Å: Chain B: S.18, T.36 Ligands: GCP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.18, B:T.36, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kessler, D., CRYSTAL STRUCTURE OF ACTIVE KRAS G12D (GPPCP) IN COMPLEX WITH THE SOAKED DIMERIC INHIBITOR BI-5747. To Be Published

Release Date

2020-11-18

Peptides

GTPase KRas: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase KRas

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