SMTL ID : 5oco.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 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 25 PLIP interactions: 25 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: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:S.35, A:S.35, A:D.48, A:D.51, A:K.165 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.8 25 PLIP interactions: 25 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: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:D.51, B:T.53, B:H.79, B:H.79 Salt bridges: B:D.137 pi-Stacking: B:F.46, B:F.46 GNP.9: 25 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, A.77, G.78, N.134, K.135, D.137, L.138, S.163, A.164, K.165 Ligands: MG.11 25 PLIP interactions: 25 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:E.49, C:T.53, C:T.53, 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:D.51, C:T.53 Salt bridges: C:D.137 pi-Stacking: C:F.46, C:F.46 pi-Cation interactions: C:K.135 GNP.12: 24 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, G.78, N.134, K.135, D.137, L.138, S.163, A.164, K.165 Ligands: MG.15 23 PLIP interactions: 23 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:T.53, D:T.53, D:T.76, D:G.78, D:N.134, D:K.135, D:K.135, D:S.163, D:A.164, D:K.165 Water bridges: D:S.35 Salt bridges: D:D.137 pi-Stacking: D:F.46, D:F.46 pi-Cation interactions: D:K.135 GNP.16: 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 23 PLIP interactions: 23 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:T.53, E:G.78, E:N.134, E:K.135, E:K.135, E:A.164, E:K.165 Water bridges: 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.21 23 PLIP interactions: 23 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: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:K.165 Salt bridges: F:D.137 pi-Stacking: F:F.46, F:F.46

5 x 9RK: ~{N}-[[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]furan-2-carboxamide(Non-covalent)

9RK.2: 10 residues within 4Å: Chain A: K.23, L.24, V.25, E.55, S.57, D.72, L.74, Y.89, T.92, G.93 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.23, A:V.25, A:E.55, A:E.55, A:L.74, A:T.92 Hydrogen bonds: A:E.55, A:E.55, A:S.57 9RK.10: 10 residues within 4Å: Chain C: K.23, L.24, V.25, E.55, S.57, D.72, L.74, Y.89, T.92, G.93 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:K.23, C:V.25, C:E.55, C:L.74, C:T.92 Hydrogen bonds: C:S.57 9RK.13: 10 residues within 4Å: Chain D: K.23, L.24, V.25, E.55, S.57, D.72, L.74, Y.89, T.92, G.93 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:K.23, D:V.25, D:E.55, D:E.55, D:L.74, D:T.92 Hydrogen bonds: D:E.55, D:E.55, D:S.57 9RK.17: 8 residues within 4Å: Chain E: K.23, L.24, E.55, S.57, D.72, L.74, Y.89, T.92 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:K.23, E:E.55, E:L.74, E:T.92 Hydrogen bonds: E:T.92 pi-Cation interactions: E:K.23 9RK.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 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:K.23, F:V.25, F:L.74, F:T.92 Hydrogen bonds: F:S.57, F:T.92

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

PEG.3: 2 residues within 4Å: Chain A: R.153, S.154 No protein-ligand interaction detected (PLIP)

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: S.35, T.53 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.2 MG.8: 3 residues within 4Å: Chain B: S.35, T.53 Ligands: GNP.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.35, B:T.53, H2O.7, H2O.7 MG.11: 3 residues within 4Å: Chain C: S.35, T.53 Ligands: GNP.9 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.35, C:T.53, H2O.11, H2O.12 MG.15: 3 residues within 4Å: Chain D: S.35, T.53 Ligands: GNP.12 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.35, D:T.53, H2O.14, H2O.14 MG.18: 4 residues within 4Å: Chain E: S.35, T.53, D.75 Ligands: GNP.16 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.35, E:T.53, H2O.16, H2O.17 MG.21: 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.19, H2O.19

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

CIT.6: 3 residues within 4Å: Chain B: R.141, D.144, T.145 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.144, B:T.145, B:T.145 Water bridges: B:R.141, B:K.146 Salt bridges: B:R.141 CIT.7: 4 residues within 4Å: Chain B: H.113, E.116, Q.117, R.120 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:E.116 Hydrogen bonds: B:Q.117, B:R.120 Salt bridges: B:H.113, B:H.113, B:R.120 CIT.14: 4 residues within 4Å: Chain D: H.113, E.116, Q.117, R.120 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.113, D:E.116, D:Q.117 Salt bridges: D:H.113, D:H.113, D:R.120

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
B

B
A

C
C

D
D

E
E

F
F

GTPase KRas

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