MolNFT v1 · #182168 · protein

Mouse CTPS2-I250T bound to inhibitor R80

7MIV · CTP synthase 2: “Mouse CTPS2-I250T bound to inhibitor R80”. Electron microscopy, 4 ligands (GLN, UTP, ZG4), 20 pockets (best druggability 0.83). MolNFT v1 #182168 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7MIV
Type: protein
Length: 2,168 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CTP synthase 2
EC: 6.3.4.2
UniProt: P70303
Ligands: GLN, UTP, ZG4, MG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 1 distinct chain · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, C, H, G	CTP synthase 2 (EC 6.3.4.2)	protein	542	42% helix, 21% strand	P70303

Ligands and binding sites

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

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	903	0.83	0.85	72	MG, UTP, ZG4
2	1032	0.83	0.84	76	MG, UTP, ZG4
3	1028	0.83	0.84	77	ZG4, UTP, MG
4	1159	0.81	0.82	88	ZG4, UTP, MG
5	287	0.80	0.91	61	empty

Interfaces

6 interfaces between chains.

D–H · 1325 Å² buried · 30 hydrogen bonds · protein-protein
C–G · 1324 Å² buried · 32 hydrogen bonds · protein-protein
D–C · 896 Å² buried · 6 hydrogen bonds · protein-protein
H–G · 896 Å² buried · 6 hydrogen bonds · protein-protein
D–G · 477 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7MIV · Mouse CTPS2-I250T bound to inhibitor R80 · the same entry in another collection · chain G against G, TM-score 1.00
P70303 · AlphaFold monomer V2.0 prediction for CTP synthase 2 (P70303) · a predicted model of the same protein · chain H 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 P70303
Elsewhere: RCSB PDB 7MIV · PDBe 7MIV · UniProt P70303

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