SMTL ID : 5ocg.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.18, T.36 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, A:T.36, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain A: G.11, A.60, G.61, Y.97 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.11, A:A.60, A:G.61, A:Y.97, H2O.3, H2O.3

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

GNP.2: 24 residues within 4Å: Chain A: A.12, D.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, P.35, T.36, G.61, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.1 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:D.13, A:G.14, A:V.15, A:G.16, A:K.17, A:K.17, A:K.17, A:S.18, A:A.19, A:E.32, A:T.36, A:T.36, A:G.61, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:D.13, A:S.18, A:S.18, A:Y.33, A:D.34 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29

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

9R5.3: 8 residues within 4Å: Chain A: K.6, L.7, E.38, D.55, L.57, Q.71, Y.72, T.75 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.57, A:T.75 Hydrogen bonds: A:E.38, A:T.75 Halogen bonds: A:D.55

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: F.91, E.92, H.95, L.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.91, A:H.95 Water bridges: A:H.95

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

PEG.6: 7 residues within 4Å: Chain A: R.69, M.73, K.89, D.93, H.96, Y.97, Q.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.89, A:D.93, A:H.96 Water bridges: A:D.93

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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