SMTL ID : 6fa3.1 (5 other biounits)

Antibody derived (Abd-6) small molecule binding to KRAS.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.21, T.39, D.61 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.1

1 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 23 PLIP interactions: 23 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:G.64, A:N.120, A:K.121, A:K.121, A:A.150, A:K.151 Water bridges: A:S.21, A:S.21, A:D.37, A:T.39 Salt bridges: A:D.123 pi-Stacking: A:F.32, A:F.32 pi-Cation interactions: A:K.121

1 x D1Z: ~{N}-[[(3~{R})-5-[5-[[3-[(dimethylamino)methyl]phenyl]amino]-6-methoxy-pyridin-2-yl]-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]oxane-4-carboxamide(Non-covalent)

D1Z.3: 13 residues within 4Å: Chain A: K.9, L.10, V.11, S.43, Y.44, R.45, D.58, I.59, L.60, Q.74, Y.75, T.78, G.79 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.9, A:V.11, A:R.45, A:D.58, A:L.60, A:Q.74, A:T.78 pi-Cation interactions: A: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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

GTPase KRas

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