SMTL ID : 6fa2.4 (5 other biounits)

Antibody derived (Abd-5) small molecule binding to KRAS.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.20, D.60, T.61 Ligands: GNP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.20

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

GNP.2: 23 residues within 4Å: Chain A: A.14, G.15, G.16, V.17, G.18, K.19, S.20, A.21, F.31, V.32, D.33, E.34, Y.35, A.62, G.63, N.119, K.120, D.122, L.123, S.148, A.149, K.150 Ligands: MG.1 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.16, A:V.17, A:G.18, A:K.19, A:K.19, A:K.19, A:S.20, A:A.21, A:V.32, A:Y.35, A:G.63, A:N.119, A:K.120, A:K.120, A:S.148, A:A.149, A:K.150 Salt bridges: A:D.122 pi-Stacking: A:F.31, A:F.31 pi-Cation interactions: A:K.120

1 x D2W: 4-[2-(dimethylamino)ethoxy]-~{N}-[[(3~{R})-5-(6-methoxypyridin-2-yl)-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]benzamide(Non-covalent)

D2W.3: 10 residues within 4Å: Chain A: K.8, L.9, V.10, S.42, Y.43, D.57, I.58, L.59, Y.74, T.77 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.8, A:V.10, A:D.57, A:L.59

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

2018-09-05

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

GTPase KRas

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