SMTL ID : 6f76.1

Antibody derived (Abd-8) small molecule binding to KRAS.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.21, T.39 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.21, A:T.39, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain B: S.21, T.39 Ligands: GNP.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.21, B:T.39, H2O.1, H2O.1 MG.7: 3 residues within 4Å: Chain C: S.21, T.39 Ligands: GNP.8 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.21, C:T.39, H2O.2, H2O.2 MG.11: 4 residues within 4Å: Chain D: S.21, T.39, D.61 Ligands: GNP.10 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.21, D:T.39, H2O.2, H2O.2 MG.12: 3 residues within 4Å: Chain E: S.21, T.39 Ligands: GNP.13 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.21, E:T.39, H2O.2, H2O.2 MG.14: 5 residues within 4Å: Chain F: S.21, T.39, D.61, T.62 Ligands: GNP.15 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:S.21, F:T.39

6 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.2: 25 residues within 4Å: Chain A: A.15, G.16, G.17, V.18, G.19, K.20, S.21, A.22, F.32, V.33, D.34, E.35, Y.36, P.38, T.39, A.63, G.64, N.120, K.121, D.123, L.124, S.149, A.150, K.151 Ligands: MG.1 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.17, A:V.18, A:G.19, A:K.20, A:K.20, A:S.21, A:A.22, A:V.33, A:T.39, A:T.39, A:G.64, A:N.120, A:K.121, A:K.121, A:A.150, A:K.151 Water bridges: A:S.21, A:S.21, A:D.37 Salt bridges: A:D.123 pi-Stacking: A:F.32, A:F.32 pi-Cation interactions: A:K.121 GNP.5: 25 residues within 4Å: Chain B: A.15, G.16, G.17, V.18, G.19, K.20, S.21, A.22, F.32, V.33, D.34, E.35, Y.36, P.38, T.39, A.63, G.64, N.120, K.121, D.123, L.124, S.149, A.150, K.151 Ligands: MG.4 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.17, B:V.18, B:G.19, B:K.20, B:K.20, B:S.21, B:A.22, B:V.33, B:T.39, B:G.64, B:N.120, B:K.121, B:K.121, B:A.150, B:K.151 Water bridges: B:S.21, B:S.21, B:S.21, B:D.37, B:T.39 Salt bridges: B:D.123 pi-Stacking: B:F.32, B:F.32 pi-Cation interactions: B:K.121 GNP.8: 26 residues within 4Å: Chain C: A.15, G.16, G.17, V.18, G.19, K.20, S.21, A.22, F.32, V.33, D.34, E.35, Y.36, P.38, T.39, T.62, A.63, G.64, N.120, K.121, D.123, L.124, S.149, A.150, K.151 Ligands: MG.7 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:G.17, C:V.18, C:G.19, C:K.20, C:K.20, C:K.20, C:S.21, C:S.21, C:A.22, C:V.33, C:Y.36, C:T.39, C:G.64, C:N.120, C:K.121, C:K.121, C:S.149, C:A.150, C:K.151 Water bridges: C:T.39, C:T.39 Salt bridges: C:D.123 pi-Stacking: C:F.32, C:F.32 pi-Cation interactions: C:K.121 GNP.10: 25 residues within 4Å: Chain D: A.15, G.16, G.17, V.18, G.19, K.20, S.21, A.22, F.32, V.33, D.34, E.35, Y.36, P.38, T.39, A.63, G.64, N.120, K.121, D.123, L.124, S.149, A.150, K.151 Ligands: MG.11 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:G.17, D:V.18, D:G.19, D:K.20, D:K.20, D:S.21, D:A.22, D:V.33, D:T.39, D:T.62, D:G.64, D:N.120, D:K.121, D:K.121, D:S.149, D:A.150, D:K.151 Water bridges: D:K.20, D:S.21, D:T.39 Salt bridges: D:D.123 pi-Stacking: D:F.32, D:F.32 pi-Cation interactions: D:K.121 GNP.13: 25 residues within 4Å: Chain E: A.15, G.16, G.17, V.18, G.19, K.20, S.21, A.22, F.32, V.33, D.34, E.35, Y.36, P.38, T.39, A.63, G.64, N.120, K.121, D.123, L.124, S.149, A.150, K.151 Ligands: MG.12 26 PLIP interactions: 26 interactions with chain E Hydrogen bonds: E:G.17, E:V.18, E:G.19, E:K.20, E:K.20, E:K.20, E:S.21, E:A.22, E:V.33, E:Y.36, E:T.39, E:G.64, E:N.120, E:K.121, E:K.121, E:S.149, E:A.150, E:K.151 Water bridges: E:S.21, E:S.21, E:T.39, E:T.39 Salt bridges: E:D.123 pi-Stacking: E:F.32, E:F.32 pi-Cation interactions: E:K.121 GNP.15: 25 residues within 4Å: Chain F: A.15, G.16, G.17, V.18, G.19, K.20, S.21, A.22, F.32, V.33, D.34, E.35, Y.36, P.38, T.39, A.63, G.64, N.120, K.121, D.123, L.124, S.149, A.150, K.151 Ligands: MG.14 21 PLIP interactions: 21 interactions with chain F Hydrogen bonds: F:G.17, F:V.18, F:G.19, F:K.20, F:K.20, F:K.20, F:S.21, F:A.22, F:V.33, F:Y.36, F:T.39, F:G.64, F:N.120, F:K.121, F:K.121, F:A.150, F:K.151 Salt bridges: F:D.123 pi-Stacking: F:F.32, F:F.32 pi-Cation interactions: F:K.121

4 x CVK: 4-(2,3-dihydro-1,4-benzodioxin-5-yl)-~{N}-[3-[(dimethylamino)methyl]phenyl]-2-methoxy-aniline(Non-covalent)

CVK.3: 10 residues within 4Å: Chain A: K.9, L.10, V.11, S.43, R.45, D.58, L.60, Y.75, T.78 Chain E: Q.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.9, A:V.11, A:R.45, A:D.58, A:L.60, A:T.78 Hydrogen bonds: A:R.45 CVK.6: 13 residues within 4Å: Chain B: K.9, L.10, V.11, S.43, Y.44, R.45, D.58, I.59, L.60, Y.75, T.78, G.79 Chain C: Q.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:K.9, B:V.11, B:R.45, B:D.58, B:L.60, B:L.60 pi-Cation interactions: B:R.45 CVK.9: 14 residues within 4Å: Chain B: Q.3, E.7 Chain C: E.7, K.9, L.10, V.11, S.43, Y.44, R.45, D.58, I.59, L.60, Y.75, T.78 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:K.9, C:V.11, C:R.45, C:D.58, C:L.60, C:L.60, C:T.78 Hydrogen bonds: C:T.78 CVK.16: 11 residues within 4Å: Chain D: Q.3 Chain F: K.9, L.10, V.11, S.43, R.45, D.58, L.60, Y.75, T.78, G.79 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:K.9, F:V.11, F:R.45, F:D.58, F:L.60, F:L.60, F:T.78 Hydrogen bonds: F:T.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bery, N. et al., BRET-based RAS biosensors that show a novel small molecule is an inhibitor of RAS-effector protein-protein interactions. Elife (2018)

Release Date

2018-08-08

Peptides

GTPase KRas: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

E
E

F
F

GTPase KRas

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