SMTL ID : 6gog.1

KRAS-169 Q61H GPPNHP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-hexamer

Ligands

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

GNP.1: 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.2 25 PLIP interactions: 25 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: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:Y.36, A:D.37, A:T.39, A:T.39 Salt bridges: A:D.123 pi-Stacking: A:F.32, A:F.32 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.6 23 PLIP interactions: 23 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: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:D.37, B:K.151 Salt bridges: B:D.123 pi-Stacking: B:F.32, B:F.32 GNP.7: 25 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, A.63, G.64, N.120, K.121, D.123, L.124, S.149, A.150, K.151 Ligands: MG.8 24 PLIP interactions: 24 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:A.22, C:E.35, 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:S.21, C:S.21, C:D.37, C:K.151 Salt bridges: C:D.123 pi-Stacking: C:F.32, C:F.32 GNP.9: 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.10 23 PLIP interactions: 23 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.39, D:G.64, D:N.120, D:K.121, D:K.121, D:A.150, D:K.151 Water bridges: D:S.21, D:S.21, D:D.37 Salt bridges: D:D.123 pi-Stacking: D:F.32, D:F.32 pi-Cation interactions: D:K.121 GNP.12: 26 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, T.62, A.63, G.64, N.120, K.121, D.123, L.124, S.149, A.150, K.151 Ligands: MG.13 22 PLIP interactions: 22 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:T.39, E:G.64, E:N.120, E:K.121, E:K.121, E:A.150, E:K.151 Water bridges: E:S.21, E:S.21, E:D.37 Salt bridges: E:D.123 pi-Stacking: E:F.32, E:F.32 GNP.14: 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.15 27 PLIP interactions: 27 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:T.39, F:T.39, F:G.64, F:N.120, F:K.121, F:K.121, F:S.149, F:A.150, F:K.151 Water bridges: F:S.21, F:S.21, F:D.34, F:D.34, F:D.37, F:T.39 Salt bridges: F:D.123 pi-Stacking: F:F.32, F:F.32

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.21, T.39, D.61 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.21, A:T.39, H2O.1, H2O.3 MG.6: 4 residues within 4Å: Chain B: S.21, T.39, D.61 Ligands: GNP.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.21, B:T.39, H2O.8, H2O.9 MG.8: 3 residues within 4Å: Chain C: S.21, T.39 Ligands: GNP.7 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.21, C:T.39, H2O.14, H2O.14 MG.10: 3 residues within 4Å: Chain D: S.21, T.39 Ligands: GNP.9 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.21, D:T.39, H2O.17, H2O.17 MG.13: 4 residues within 4Å: Chain E: S.21, T.39, D.61 Ligands: GNP.12 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.21, E:T.39, H2O.20, H2O.20 MG.15: 4 residues within 4Å: Chain F: S.21, T.39, D.61 Ligands: GNP.14 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:S.21, F:T.39, H2O.23, H2O.24

3 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 3 residues within 4Å: Chain A: R.127, D.130, T.131 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.130, A:T.131, A:T.131 Water bridges: A:R.127, A:K.132 Salt bridges: A:R.127 CIT.4: 4 residues within 4Å: Chain A: H.99, E.102, Q.103, R.106 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.103 Water bridges: A:E.102, A:R.106, A:R.106 Salt bridges: A:H.98, A:H.99, A:H.99, A:R.106 CIT.11: 4 residues within 4Å: Chain D: H.99, E.102, Q.103, R.106 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:E.102 Hydrogen bonds: D:Q.103 Salt bridges: D:R.72, D:H.99, D:R.106, D:R.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cruz-Migoni, A. et al., Structure-based development of new RAS-effector inhibitors from a combination of active and inactive RAS-binding compounds. Proc. Natl. Acad. Sci. U.S.A. (2019)

Release Date

2019-02-06

Peptides

GTPase KRas: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

GTPase KRas