SMTL ID : 9x53.1

Crystal structure of RhoGDI2 in complex with Compound HR3119

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x 01: (3~{R})-~{N}-[2-[[(~{R})-[4-(2-fluorophenyl)phenyl]-thiophen-2-yl-methyl]amino]-2-oxidanylidene-ethyl]pyrrolidine-3-carboxamide

01.1: 14 residues within 4Å: Chain A: L.41, Y.47, Q.67, T.69, R.71, V.74, D.77, E.101, A.102, P.103, Y.112, N.114, W.131, L.133 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.41, A:Y.47, A:T.69, A:D.77, A:P.103, A:Y.112, A:Y.112, A:W.131 Hydrogen bonds: A:D.77, A:D.77, A:E.101 Water bridges: A:E.101

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

EDO.2: 7 residues within 4Å: Chain A: T.13, L.14, V.15, C.16, G.21, P.22, I.23 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.16, A:I.23, A:I.23 EDO.3: 2 residues within 4Å: Chain A: Y.86, E.94 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.86, A:Y.86 Water bridges: A:E.94 EDO.4: 2 residues within 4Å: Chain A: D.125, S.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.125, A:S.128 Water bridges: A:K.115, A:S.128 EDO.5: 3 residues within 4Å: Chain A: V.83, G.84, S.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.85, A:S.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, M. et al., Fragment-Based Discovery of a Small-Molecule RhoGDI2 Ligand, HR3119, that Inhibits Cancer Cell Migration. Acs Chem.Biol. (2025)

Release Date

2025-10-29

Peptides

Rho GDP-dissociation inhibitor 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Rho GDP-dissociation inhibitor 2

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