SMTL ID : 8v9m.2 (1 other biounit)

Human Ornithine Aminotransferase cocrystallized with its inhibitor, (R)-3-amino-5,5-difluorocyclohex-1-ene-1-carboxylic acid.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-dimer

Ligands

2 x YR5: 3-fluoro-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]benzoic acid(Non-covalent)

YR5.1: 18 residues within 4Å: Chain A: Y.20, Y.50, T.106, G.107, V.108, F.142, W.143, G.144, E.195, E.200, D.228, I.230, Q.231, K.257, R.378 Chain B: G.285, S.286, T.287 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:E.195, A:E.200 Hydrogen bonds: A:Y.20, A:T.106, A:G.107, A:V.108, A:Q.231, A:K.257, B:T.287, B:T.287, B:T.287 Salt bridges: A:K.257 pi-Stacking: A:Y.50, A:F.142 Water bridges: B:Y.288 YR5.4: 17 residues within 4Å: Chain A: G.285, S.286, T.287 Chain B: Y.20, Y.50, T.106, G.107, V.108, F.142, W.143, G.144, E.195, E.200, D.228, I.230, Q.231, K.257 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.195, B:E.200 Hydrogen bonds: B:Y.50, B:G.107, B:V.108, B:Q.231, B:K.257, A:T.287, A:T.287, A:T.287 Water bridges: B:T.106, B:T.106, B:E.200, A:Y.288 Salt bridges: B:K.257 pi-Stacking: B:Y.50, B:F.142

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: T.237, Y.245, D.315, R.322, K.339, G.340 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.237, A:Y.245, A:D.315, A:R.322, A:G.340 Water bridges: A:D.315, A:R.322 GOL.3: 8 residues within 4Å: Chain A: W.121, R.215, C.218, T.219, Q.222, V.223, L.224, D.251 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.215, A:V.223, A:D.251 Water bridges: A:Q.222, A:Q.222 GOL.5: 6 residues within 4Å: Chain B: S.151, F.165, M.166, P.167, G.168, F.169 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.151, B:F.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Devitt, A.N. et al., Design, Synthesis, and Mechanistic Studies of ( R )-3-Amino-5,5-difluorocyclohex-1-ene-1-carboxylic Acid as an Inactivator of Human Ornithine Aminotransferase. Acs Chem.Biol. (2024)

Release Date

2024-05-08

Peptides

Ornithine aminotransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Ornithine aminotransferase, mitochondrial

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