SMTL ID : 7aca.2 (1 other biounit)

CRYSTAL STRUCTURE OF AN ACTIVE KRAS G12D (GPPCP) DIMER IN COMPLEX WITH BI-5747

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 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.4: 3 residues within 4Å: Chain B: S.18, T.36 Ligands: GCP.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.18, B:T.36, H2O.6, H2O.6

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

GCP.2: 25 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, A.60, G.61, 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: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: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:D.34, A:Q.62, A:Q.62 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29 GCP.5: 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.4 28 PLIP interactions: 27 interactions with chain B, 1 interactions with chain A 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:T.36, B:G.61, B:N.117, B:K.118, B:K.118, B:A.147, B:K.148 Water bridges: B:D.13, B:D.31, B:D.31, B:Y.33, B:Y.33, B:D.34, B:T.36, B:T.36, B:Q.62, A:S.40 Salt bridges: B:D.120 pi-Stacking: B:F.29, B:F.29

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.3: 15 residues within 4Å: Chain A: M.2, E.4, K.6, L.7, V.8, E.38, S.40, R.42, L.53, D.55, L.57, Q.71, Y.72, T.75, G.76 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:M.2, A:K.6, A:K.6, A:V.8, A:R.42, A:L.57, A:L.57, A:Q.71, A:T.75 Hydrogen bonds: A:E.4, A:E.4, A:E.4, A:D.55, A:D.55, A:T.75 pi-Cation interactions: A:K.6

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 2 residues within 4Å: Chain B: E.38, S.40 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kessler, D., CRYSTAL STRUCTURE OF AN ACTIVE KRAS G12D (GPPCP) DIMER IN COMPLEX WITH BI-5747. To Be Published

Release Date

2020-11-18

Peptides

GTPase KRas: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

GTPase KRas

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