MolNFT v1 · #182152 · protein

Human CTPS1 bound to inhibitor R80

7MIF · CTP synthase 1: “Human CTPS1 bound to inhibitor R80”. Electron microscopy, 4 ligands (GLN, ZG4, UTP), 20 pockets (best druggability 0.80). MolNFT v1 #182152 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7MIF
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: GLN, ZG4, UTP, MG
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 1 distinct chain · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, G, H, I	CTP synthase 1 (EC 6.3.4.2)	protein	533	39% helix, 21% strand	P17812

Ligands and binding sites

GLN · Glutamine · ligand · 4 copies · chains C, G, H, I
ZG4 · N-(1-{2-[(cyclopropanesulfonyl)amino]-1,3-thiazol-4-yl}cyclopropyl)-5-(6-ethoxypyrazin-2-yl)pyridine-2-carboxamide · ligand · 4 copies · chains C, G, H, I
UTP · Uridine 5'-triphosphate · ligand · 4 copies · chains C, G, I, H
MG · Magnesium ion · metal · 4 copies · chains C, G, I, H

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	767	0.80	0.83	63	MG, UTP, ZG4
2	343	0.79	0.90	49	MG, UTP
3	347	0.79	0.89	51	MG, UTP
4	135	0.73	0.93	20	empty
5	162	0.73	0.91	24	empty

Interfaces

6 interfaces between chains.

G–I · 1359 Å² buried · 14 hydrogen bonds · protein-protein
C–H · 1336 Å² buried · 13 hydrogen bonds · protein-protein
H–I · 915 Å² buried · 22 hydrogen bonds · protein-protein
C–G · 835 Å² buried · 9 hydrogen bonds · protein-protein
G–H · 439 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7MIF · Human CTPS1 bound to inhibitor R80 · the same entry in another collection · chain I against I, TM-score 1.00
P17812 · AlphaFold monomer V2.0 prediction for CTP synthase 1 (P17812) · a predicted model of the same protein · chain G 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 7MIF · PDBe 7MIF · UniProt P17812

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