SMTL ID : 9x54.1

Crystal structure of RhoGDI2 in complex with Compound 3054b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: T.13, L.14, V.15, C.16, A.19, 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 GOL.2: 3 residues within 4Å: Chain A: Y.70, K.115, E.130 No protein-ligand interaction detected (PLIP)

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

01.3: 12 residues within 4Å: Chain A: L.41, Y.47, Q.67, T.69, V.74, D.77, E.101, P.103, Y.112, N.114, W.131, L.133 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.41, A:Y.47, A:D.77, A:P.103, A:Y.112, A:W.131, A:L.133 Hydrogen bonds: A:D.77, A:D.77, A:E.101

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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