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Human CTPS1 bound to inhibitor T35

Analyse Human CTPS1 bound to inhibitor T35 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MIG
Type: protein
Length: 2,132 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CTP synthase 1
EC: 6.3.4.2
UniProt: P17812
Ligands: ZFY, GLN, UTP, MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, A, B, E	CTP synthase 1 (EC 6.3.4.2)	protein	533	41% helix, 21% strand	P17812

Ligands and binding sites

ZFY · 2-{2-[(cyclopropanesulfonyl)amino]-1,3-thiazol-4-yl}-2-methyl-N-{5-[6-(trifluoromethyl)pyrazin-2-yl]pyridin-2-yl}propanamide · ligand · 4 copies · chains C, A, B, E
GLN · Glutamine · ligand · 4 copies · chains C, A, B, E
UTP · Uridine 5'-triphosphate · ligand · 4 copies · chains C, A, E, B
MG · Magnesium ion · metal · 4 copies · chains C, A, B, E

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	676	0.86	0.91	78	empty
2	300	0.78	0.90	50	MG, UTP
3	287	0.77	0.89	49	MG, UTP
4	79	0.72	0.96	21	GLN
5	189	0.72	0.89	34	MG, UTP

Interfaces

6 interfaces between chains.

A–E · 1429 Å² buried · 18 hydrogen bonds · protein-protein
C–B · 1419 Å² buried · 18 hydrogen bonds · protein-protein
C–A · 951 Å² buried · 24 hydrogen bonds · protein-protein
B–E · 946 Å² buried · 24 hydrogen bonds · protein-protein
C–E · 425 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7MIG · Human CTPS1 bound to inhibitor T35 · the same entry in another collection · chain E against E, TM-score 1.00
P17812 · AlphaFold monomer V2.0 prediction for CTP synthase 1 (P17812) · a predicted model of the same protein · chain E against A, TM-score 0.99

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 P17812
Elsewhere: RCSB PDB 7MIG · PDBe 7MIG · UniProt P17812

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