MolNFT v1 · #182162 · protein

Mouse CTPS1 bound to inhibitor R80

7MIP · CTP synthase 1: “Mouse CTPS1 bound to inhibitor R80”. Electron microscopy, 4 ligands (GLN, UTP, ZG4), 20 pockets (best druggability 0.82). MolNFT v1 #182162 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7MIP
Type: protein
Length: 2,160 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CTP synthase 1
EC: 6.3.4.2
UniProt: P70698
Ligands: GLN, UTP, ZG4, MG
Pockets: 20 · best druggability 0.82

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D, G, I	CTP synthase 1 (EC 6.3.4.2)	protein	540	41% helix, 21% strand	P70698

Ligands and binding sites

GLN · Glutamine · ligand · 4 copies · chains C, D, G, I
UTP · Uridine 5'-triphosphate · ligand · 4 copies · chains C, D, I, G
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, D, G, I
MG · Magnesium ion · metal · 4 copies · chains C, D, G, I

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	430	0.82	0.90	69	MG, UTP
2	410	0.82	0.90	61	MG, UTP
3	385	0.81	0.90	63	MG, UTP
4	331	0.79	0.89	43	MG, UTP
5	231	0.75	0.89	41	empty

Interfaces

6 interfaces between chains.

D–I · 1294 Å² buried · 24 hydrogen bonds · protein-protein
C–G · 1290 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 906 Å² buried · 6 hydrogen bonds · protein-protein
G–I · 906 Å² buried · 6 hydrogen bonds · protein-protein
C–I · 436 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7MIP · Mouse CTPS1 bound to inhibitor R80 · the same entry in another collection · chain I against I, TM-score 1.00
P70698 · AlphaFold monomer V2.0 prediction for CTP synthase 1 (P70698) · a predicted model of the same protein · chain I 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 P70698
Elsewhere: RCSB PDB 7MIP · PDBe 7MIP · UniProt P70698

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