SMTL ID : 5oct.1

Discovery of small molecules binding to KRAS via high affinity antibody fragment competition method.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-hexamer

Ligands

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

GNP.1: 25 residues within 4Å: Chain A: A.29, G.30, G.31, V.32, G.33, K.34, S.35, A.36, F.46, V.47, D.48, E.49, Y.50, P.52, T.53, A.77, G.78, N.134, K.135, D.137, L.138, S.163, A.164, K.165 Ligands: MG.4 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.31, A:V.32, A:G.33, A:K.34, A:K.34, A:S.35, A:S.35, A:A.36, A:V.47, A:T.53, A:T.53, A:G.78, A:N.134, A:K.135, A:K.135, A:S.163, A:A.164, A:K.165 Water bridges: A:D.51, A:T.53 Salt bridges: A:D.137 pi-Stacking: A:F.46, A:F.46 GNP.5: 25 residues within 4Å: Chain B: A.29, G.30, G.31, V.32, G.33, K.34, S.35, A.36, F.46, V.47, D.48, E.49, Y.50, P.52, T.53, A.77, G.78, N.134, K.135, D.137, L.138, S.163, A.164, K.165 Ligands: MG.7 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:G.31, B:V.32, B:G.33, B:K.34, B:K.34, B:S.35, B:A.36, B:V.47, B:T.53, B:T.53, B:G.78, B:N.134, B:K.135, B:K.135, B:A.164, B:K.165 Water bridges: B:S.35, B:S.35, B:D.51, B:K.165 Salt bridges: B:D.137 pi-Stacking: B:F.46 pi-Cation interactions: B:K.135 GNP.8: 26 residues within 4Å: Chain C: A.29, G.30, G.31, V.32, G.33, K.34, S.35, A.36, F.46, V.47, D.48, E.49, Y.50, P.52, T.53, T.76, A.77, G.78, N.134, K.135, D.137, L.138, S.163, A.164, K.165 Ligands: MG.10 28 PLIP interactions: 28 interactions with chain C Hydrogen bonds: C:G.31, C:V.32, C:G.33, C:K.34, C:K.34, C:K.34, C:S.35, C:A.36, C:V.47, C:Y.50, C:Y.50, C:T.53, C:T.76, C:G.78, C:N.134, C:K.135, C:K.135, C:S.163, C:A.164, C:K.165 Water bridges: C:S.35, C:S.35, C:T.53, C:T.53 Salt bridges: C:D.137 pi-Stacking: C:F.46, C:F.46 pi-Cation interactions: C:K.135 GNP.11: 25 residues within 4Å: Chain D: A.29, G.30, G.31, V.32, G.33, K.34, S.35, A.36, F.46, V.47, D.48, E.49, Y.50, P.52, T.53, A.77, G.78, N.134, K.135, D.137, L.138, S.163, A.164, K.165 Ligands: MG.14 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:G.31, D:V.32, D:G.33, D:K.34, D:K.34, D:S.35, D:A.36, D:V.47, D:Y.50, D:T.53, D:T.53, D:G.78, D:N.134, D:K.135, D:K.135, D:S.163, D:A.164, D:K.165 Water bridges: D:D.51, D:K.165, D:K.165 Salt bridges: D:D.137 pi-Stacking: D:F.46, D:F.46 pi-Cation interactions: D:K.135 GNP.15: 25 residues within 4Å: Chain E: A.29, G.30, G.31, V.32, G.33, K.34, S.35, A.36, F.46, V.47, D.48, E.49, Y.50, P.52, T.53, A.77, G.78, N.134, K.135, D.137, L.138, S.163, A.164, K.165 Ligands: MG.18 27 PLIP interactions: 27 interactions with chain E Hydrogen bonds: E:G.31, E:V.32, E:G.33, E:K.34, E:K.34, E:K.34, E:S.35, E:A.36, E:V.47, E:Y.50, E:Y.50, E:T.53, E:T.53, E:G.78, E:N.134, E:K.135, E:K.135, E:S.163, E:A.164, E:K.165 Water bridges: E:S.35, E:S.35, E:D.51 Salt bridges: E:D.137 pi-Stacking: E:F.46, E:F.46 pi-Cation interactions: E:K.135 GNP.19: 25 residues within 4Å: Chain F: A.29, G.30, G.31, V.32, G.33, K.34, S.35, A.36, F.46, V.47, D.48, E.49, Y.50, P.52, T.53, A.77, G.78, N.134, K.135, D.137, L.138, S.163, A.164, K.165 Ligands: MG.23 25 PLIP interactions: 25 interactions with chain F Hydrogen bonds: F:G.31, F:V.32, F:G.33, F:K.34, F:K.34, F:K.34, F:S.35, F:A.36, F:V.47, F:Y.50, F:Y.50, F:T.53, F:G.78, F:N.134, F:K.135, F:K.135, F:S.163, F:A.164, F:K.165 Water bridges: F:S.35, F:S.35, F:D.51 Salt bridges: F:D.137 pi-Stacking: F:F.46, F:F.46

9 x 9R5: [(2~{R})-6-chloranyl-2,3-dihydro-1,4-benzodioxin-2-yl]methanamine(Non-covalent)

9R5.2: 5 residues within 4Å: Chain A: H.79, D.110, H.113, Y.114, Q.117 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.79, A:H.113 pi-Stacking: A:H.79, A:Y.114 Halogen bonds: A:Q.117 9R5.6: 8 residues within 4Å: Chain B: K.23, V.25, S.57, R.59, D.72, L.74, T.92, G.93 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.23, B:L.74 Hydrogen bonds: B:S.57, B:D.72 pi-Cation interactions: B:K.23 9R5.9: 7 residues within 4Å: Chain C: V.25, S.57, D.72, L.74, Y.89, T.92, G.93 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:D.72, C:L.74 Hydrogen bonds: C:S.57, C:D.72 Halogen bonds: C:Y.89 9R5.12: 7 residues within 4Å: Chain D: V.25, S.57, D.72, L.74, Y.89, T.92, G.93 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:D.72, D:L.74 Hydrogen bonds: D:S.57, D:D.72 pi-Cation interactions: D:K.23 Halogen bonds: D:Y.89 9R5.13: 5 residues within 4Å: Chain D: R.86, D.110, H.113, Y.114, Q.117 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:H.113 9R5.16: 10 residues within 4Å: Chain E: K.23, L.24, V.25, S.57, R.59, D.72, L.74, Y.89, T.92, G.93 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:K.23, E:D.72, E:L.74 Hydrogen bonds: E:S.57, E:D.72 pi-Cation interactions: E:K.23 Halogen bonds: E:Y.89 9R5.17: 6 residues within 4Å: Chain E: R.86, K.106, D.110, H.113, Y.114, Q.117 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:H.113 Hydrogen bonds: E:K.106, E:D.110 pi-Stacking: E:Y.114 9R5.20: 9 residues within 4Å: Chain F: K.23, L.24, V.25, S.57, D.72, L.74, Y.89, T.92, G.93 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:K.23, F:D.72, F:L.74 Hydrogen bonds: F:S.57 pi-Cation interactions: F:K.23 9R5.21: 6 residues within 4Å: Chain F: R.86, K.106, D.110, H.113, Y.114, Q.117 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:D.110, F:H.113 Hydrogen bonds: F:K.106, F:K.106 pi-Stacking: F:Y.114

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 9 residues within 4Å: Chain A: I.160, E.161, Q.168, G.169, D.172 Chain B: Q.40, N.44, F.46, K.165 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.161, A:Q.168, B:Q.40, B:Q.40 Water bridges: A:G.169, A:G.169

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: S.35, T.53, D.75 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.35, A:T.53, H2O.1, H2O.1 MG.7: 4 residues within 4Å: Chain B: S.35, T.53, D.75 Ligands: GNP.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.35, B:T.53, H2O.4, H2O.4 MG.10: 4 residues within 4Å: Chain C: S.35, T.53, D.75 Ligands: GNP.8 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.35, C:T.53, H2O.7, H2O.8 MG.14: 4 residues within 4Å: Chain D: S.35, T.53, D.75 Ligands: GNP.11 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.35, D:T.53, H2O.9, H2O.9 MG.18: 4 residues within 4Å: Chain E: S.35, T.53, D.75 Ligands: GNP.15 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.35, E:T.53, H2O.11, H2O.12 MG.23: 4 residues within 4Å: Chain F: S.35, T.53, D.75 Ligands: GNP.19 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:S.35, F:T.53, H2O.13, H2O.13

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.22: 6 residues within 4Å: Chain F: T.105, F.108, T.142, V.143, D.144, Q.147 No protein-ligand interaction detected (PLIP)

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

GTPase KRas

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