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(1S,3S)-3-amino-4-(perfluoropropan-2-YLIDENE)CYCLOPENTANE-1-carboxylic acid hydrochloride, a potent inhibitor of ornithine aminotransferase

Analyse (1S,3S)-3-amino-4-(perfluoropropan-2-YLIDENE)CYCLOPENTANE-1-carboxylic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OIA
Type: protein
Length: 1,212 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ornithine aminotransferase, mitochondrial
EC: 2.6.1.13
UniProt: P04181
Ligands: PLP, MQ4
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Ornithine aminotransferase, mitochondrial (EC 2.6.1.13)	protein	404	38% helix, 20% strand	P04181

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
MQ4 · (1S)-3-amino-4-[(2S)-1,1,1-trifluoro-3-oxopropan-2-yl]cyclopent-3-ene-1-carboxylic acid · ligand · 2 copies · chains A, B, C
GOL · Glycerol · additive · 2 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	444	0.78	0.86	56	PLP, MQ4
2	405	0.76	0.85	56	PLP
3	768	0.72	0.78	53	GOL
4	262	0.56	0.77	38	PLP, MQ4
5	286	0.55	0.76	28	empty

Interfaces

3 interfaces between chains.

A–B · 5301 Å² buried · 76 hydrogen bonds · protein-protein
B–C · 677 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 220 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

6OIA · (1S,3S)-3-amino-4-(perfluoropropan-2-ylidene)cyclopentane-1-carboxylic acid… · the same entry in another collection · chain A against A, TM-score 1.00
P04181 · AlphaFold monomer V2.0 prediction for ornithine aminotransferase, mitochondrial (P04181) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P04181
Elsewhere: RCSB PDB 6OIA · PDBe 6OIA · UniProt P04181

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