Research workbench

Kynurenine aminotransferase II inhibitors

Analyse Kynurenine aminotransferase II inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GE9
Type: protein
Length: 1,712 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: KYNURENINE/ALPHA-aminoadipate aminotransferase, mitochondrial
EC: 2.6.1.39, 2.6.1.7
UniProt: Q8N5Z0
Ligands: 0L0
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	KYNURENINE/ALPHA-aminoadipate aminotransferase, mitochondrial (EC 2.6.1.39, 2.6.1.7)	protein	428	43% helix, 17% strand	Q8N5Z0

Ligands and binding sites

0L0 · (4-{[(6-benzyl-1-hydroxy-7-methoxy-2-oxo-1,2-dihydroquinolin-3-yl)amino]methyl}-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	258	0.82	0.94	36	0L0
2	254	0.81	0.93	40	0L0
3	245	0.81	0.94	34	0L0
4	212	0.81	0.94	34	0L0
5	339	0.67	0.81	33	empty

Interfaces

4 interfaces between chains.

C–D · 4307 Å² buried · 73 hydrogen bonds · protein-protein
A–B · 4262 Å² buried · 69 hydrogen bonds · protein-protein
A–C · 279 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 101 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4GE9 · Kynurenine Aminotransferase II Inhibitors · the same entry in another collection · chain D against D, TM-score 1.00
Q8N5Z0 · AlphaFold monomer V2.0 prediction for KYNURENINE/ALPHA-aminoadipate aminotransferase… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q8N5Z0
Elsewhere: RCSB PDB 4GE9 · PDBe 4GE9 · UniProt Q8N5Z0

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