Research workbench

CPS1 bound to allosteric inhibitor H3B-193

Analyse CPS1 bound to allosteric inhibitor H3B-193 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UEL
Type: protein
Length: 2,665 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carbamoyl-phosphate synthase [ammonia], mitochondrial
EC: 6.3.4.16
UniProt: P31327
Ligands: Q5A, ZN
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Carbamoyl-phosphate synthase [ammonia], mitochondrial (EC 6.3.4.16)	protein	1333	32% helix, 24% strand	P31327
B	Carbamoyl-phosphate synthase [ammonia], mitochondrial (EC 6.3.4.16)	protein	1332	33% helix, 24% strand	P31327

Ligands and binding sites

Q5A · N~1~-[(4-fluorophenyl)methyl]-N~1~-methyl-N~4~-(4-methyl-1,3-thiazol-2-yl)piperidine-1,4-dicarboxamide · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	859	0.85	0.87	107	empty
2	1062	0.85	0.86	133	empty
3	281	0.83	0.94	39	empty
4	617	0.81	0.86	80	empty
5	500	0.80	0.87	64	empty

Interfaces

1 interface between chains.

A–B · 223 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6UEL · CPS1 bound to allosteric inhibitor H3B-193 · the same entry in another collection · chain A against A, TM-score 1.00
P31327 · AlphaFold monomer V2.0 prediction for carbamoyl-phosphate synthase [ammonia]… · 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 P31327
Elsewhere: RCSB PDB 6UEL · PDBe 6UEL · UniProt P31327

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