SMTL ID : 9b8n.1

Crystal structure of ornithine decarboxylase in complex with a novel inhibitor (10-S)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 17 residues within 4Å: Chain A: A.67, K.69, D.88, A.111, R.154, L.166, H.197, S.200, G.236, G.237, E.274, P.275, G.276, R.277, Y.389 Chain B: C.360 Ligands: 01.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.237, A:G.276, A:R.277, A:Y.389, A:Y.389 Water bridges: A:F.238, A:F.238 Salt bridges: A:H.197, A:R.277 pi-Cation interactions: A:K.69, A:H.197 PLP.3: 15 residues within 4Å: Chain A: C.360 Chain B: 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 Ligands: 01.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.237, B:G.276, B:R.277, B:Y.389, B:Y.389 Water bridges: B:F.238 Salt bridges: B:H.197, B:R.277 pi-Stacking: B:H.197

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

01.2: 11 residues within 4Å: Chain A: K.69, L.166, S.200, R.277, Y.331, D.332, Y.389 Chain B: Y.323, C.360, D.361 Ligands: PLP.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.389, B:D.361 Hydrogen bonds: A:D.332 01.4: 7 residues within 4Å: Chain A: C.360, D.361 Chain B: H.197, Y.331, D.332, Y.389 Ligands: PLP.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.332

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

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