SMTL ID : 7acq.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-trimer

Ligands

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

GDP.1: 19 residues within 4Å: Chain A: A.12, 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.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:A.147, A:K.148 Water bridges: A:K.17, A:K.17, A:S.18, A:Y.33, A:Y.33, A:Y.33 Salt bridges: A:K.17, A:D.120 pi-Cation interactions: A:K.118 GDP.4: 20 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, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.5 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:A.12, B:G.14, B:V.15, B:G.16, B:K.17, B:S.18, B:A.19, B:D.31, B:N.117, B:K.118, B:K.118, B:S.146, B:A.147, B:K.148 Water bridges: B:K.17, B:Y.33, B:Y.33 Salt bridges: B:K.17, B:D.120 GDP.7: 21 residues within 4Å: Chain C: 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, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.8 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:G.14, C:V.15, C:G.16, C:K.17, C:S.18, C:A.19, C:V.30, C:N.117, C:K.118, C:K.118, C:A.147, C:K.148 Water bridges: C:K.17, C:S.18, C:S.18 Salt bridges: C:K.17, C:D.120

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.18 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.2, H2O.2, H2O.4 MG.5: 2 residues within 4Å: Chain B: S.18 Ligands: GDP.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.18, H2O.8, H2O.8, H2O.8, H2O.10 MG.8: 2 residues within 4Å: Chain C: S.18 Ligands: GDP.7 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:S.18, H2O.14, H2O.14, H2O.15, H2O.17

2 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: 29 residues within 4Å: Chain A: M.2, T.3, E.4, K.6, L.7, V.8, S.40, R.42, L.53, D.55, L.57, M.68, Q.71, Y.72, T.75 Chain B: M.2, T.3, E.4, K.6, L.7, V.8, S.40, R.42, L.53, D.55, L.57, Q.71, Y.72, T.75 30 PLIP interactions: 16 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:K.6, B:K.6, B:V.8, B:L.53, B:L.57, B:Q.71, B:Y.72, A:K.6, A:K.6, A:V.8, A:L.53, A:L.57, A:Q.71, A:Y.72 Hydrogen bonds: B:E.4, B:E.4, B:E.4, B:E.4, B:S.40, B:D.55, B:D.55, A:E.4, A:E.4, A:S.40, A:D.55, A:T.75 Water bridges: B:M.68, A:M.2 pi-Cation interactions: B:K.6, A:K.6 R6W.6: 14 residues within 4Å: Chain C: M.2, T.3, E.4, K.6, L.7, V.8, S.40, R.42, L.53, D.55, L.57, Q.71, Y.72, T.75 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:K.6, C:K.6, C:K.6, C:V.8, C:L.57, C:L.57, C:Q.71, C:Y.72 Hydrogen bonds: C:E.4, C:E.4, C:E.4, C:E.4, C:S.40, C:D.55, C:D.55 pi-Cation interactions: C:K.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kessler, D., CRYSTAL STRUCTURE OF INACTIVE KRAS G12D (GDP) IN COMPLEX WITH THE SOAKED DIMERIC INHIBITOR BI00925747. To Be Published

Release Date

2020-11-18

Peptides

GTPase KRas: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

GTPase KRas

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