SMTL ID : 9ggy.1

Human KRas4A (GDP) in complex with compound 29

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

monomer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 20 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, Y.35, N.119, K.120, D.122, L.123, S.148, A.149, K.150 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:A.14, A:G.16, A:V.17, A:G.18, A:K.19, A:S.20, A:A.21, A:V.32, A:N.119, A:K.120, A:K.120, A:A.149, A:K.150 Water bridges: A:K.19, A:K.19, A:K.19, A:K.19, A:S.20, A:S.20, A:D.33, A:Y.35, A:Y.35 Salt bridges: A:K.19, A:D.122 pi-Stacking: A:F.31, A:F.31

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.20 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.20, H2O.1, H2O.1, H2O.1, H2O.2

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: P.143, I.145, R.154, T.161 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.154, A:R.154 Water bridges: A:F.144, A:F.144 EDO.4: 4 residues within 4Å: Chain A: I.49, D.50, G.51, R.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.50, A:G.51

1 x 01: 12-(1-aza-5-azanidaspiro[4.5]decan-8-yl)-18-[(1-chloro-3-hydroxy-1,2,3-benzothiadiazol-5-yl)-lambda4-sulfanylidene]-4-hydroxy-3,3-dioxo-3lambda6-thia-1,4,12,17-tetraza-2lambda6-thia-6,10,19-triaza-3

01.5: 13 residues within 4Å: Chain A: L.9, V.10, E.40, D.41, S.42, D.57, L.59, S.68, M.70, Q.73, Y.74, T.77, G.78 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.59, A:L.59, A:M.70, A:M.70 Hydrogen bonds: A:D.41, A:D.41, A:S.42 Halogen bonds: A:Y.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parry, C.W. et al., Reversible Small Molecule Multivariant Ras Inhibitors Display Tunable Affinity for the Active and Inactive Forms of Ras. J.Med.Chem. (2025)

Release Date

2025-04-16

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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