SMTL ID : 9b8m.1

Crystal structure of ornithine decarboxylase in complex with a novel inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x 01: O-{[(3R)-pyrrolidin-3-yl]methyl}hydroxylamine

01.1: 8 residues within 4Å: Chain A: K.69, H.197, R.277, D.332, Y.389 Chain B: Y.323, D.361 Ligands: PLP.2 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.69, A:R.277, A:D.332, A:D.332 Hydrophobic interactions: B:D.361 01.3: 8 residues within 4Å: Chain A: Y.323, D.361, F.397 Chain B: K.69, L.166, D.332, Y.389 Ligands: PLP.4 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.389, A:D.361, A:F.397 Hydrogen bonds: B:D.332

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.2: 15 residues within 4Å: Chain A: A.67, K.69, D.88, R.154, H.197, S.200, G.236, G.237, E.274, P.275, G.276, R.277, Y.389 Chain B: C.360 Ligands: 01.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.237, A:G.276, A:R.277, A:Y.389, A:Y.389 Salt bridges: A:H.197, A:R.277 pi-Stacking: A:H.197 PLP.4: 16 residues within 4Å: Chain A: C.360 Chain B: A.67, K.69, D.88, R.154, L.166, H.197, S.200, G.236, G.237, E.274, P.275, G.276, R.277, Y.389 Ligands: 01.3 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.69, B:G.237, B:G.276, B:R.277, B:Y.389, B:Y.389 Salt bridges: B:H.197, B:R.277 pi-Cation interactions: B:K.69, B:H.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schultz, C.R. et al., Design, Synthesis, and Biological Activity of Novel Ornithine Decarboxylase (ODC) Inhibitors. J.Med.Chem. (2025)

Release Date

2025-03-12

Peptides

Ornithine decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ornithine decarboxylase