SMTL ID : 6fa1.1

Antibody derived (Abd-4) small molecule binding to KRAS.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

hetero-2-4-mer

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.2 MG.4: 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.5, H2O.6 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.9, H2O.9 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.11, H2O.11 MG.11: 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.13, H2O.14 MG.13: 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.15, H2O.16

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 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:A.22, A:V.33, A:T.39, A:T.39, A:G.64, A:N.120, A:K.121, A:K.121, A:S.149, A:A.150, A:K.151 Water bridges: A:S.21, A:S.21, A:Y.36, 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 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: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:S.149, B:A.150, B:K.151 Water bridges: B:T.39 Salt bridges: B:D.123 pi-Stacking: B:F.32, B:F.32 pi-Cation interactions: B:K.121 GNP.8: 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.7 27 PLIP interactions: 27 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:V.33, C:Y.36, C:T.39, C:T.62, 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 pi-Cation interactions: C:K.121 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 21 PLIP interactions: 21 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:S.149, D:A.150, D:K.151 Salt bridges: D:D.123 pi-Stacking: D:F.32, D:F.32 pi-Cation interactions: D:K.121 GNP.12: 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.11 23 PLIP interactions: 23 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:A.150, E:K.151 Water bridges: E:S.21, E:D.37 Salt bridges: E:D.123 pi-Stacking: E:F.32, E:F.32 pi-Cation interactions: E:K.121 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.13 25 PLIP interactions: 25 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:S.149, F:A.150, F:K.151 Water bridges: F:S.21, F:D.37, F:T.39, F:T.39 Salt bridges: F:D.123 pi-Stacking: F:F.32, F:F.32

3 x D2Z: 2-[4-[[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methylcarbamoyl]phenoxy]ethyl-dimethyl-azanium(Non-covalent)

D2Z.3: 10 residues within 4Å: Chain A: K.9, L.10, V.11, D.58, L.60, M.71, Q.74, Y.75, T.78, G.79 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.9, A:V.11, A:L.60, A:T.78 Hydrogen bonds: A:Q.74 D2Z.6: 3 residues within 4Å: Chain B: H.65, H.99, Y.100 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:H.99 pi-Stacking: B:H.65, B:Y.100 D2Z.15: 8 residues within 4Å: Chain F: K.9, L.10, V.11, D.58, L.60, Q.74, Y.75, T.78 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:K.9, F:V.11, F:L.60, F:Q.74, F:T.78 Hydrogen bonds: F:Q.74, F:T.78 pi-Cation interactions: F:K.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Quevedo, C.E. et al., Small molecule inhibitors of RAS-effector protein interactions derived using an intracellular antibody fragment. Nat Commun (2018)

Release Date

2018-08-22

Peptides

GTPase KRas: AE
GTPase KRas: BCDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

E
E

B
A

C
C

D
D

F
F

GTPase KRas

GTPase KRas

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