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Human CTPS2 bound to inhibitor T35

Analyse Human CTPS2 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: 7MII
Type: protein
Length: 1,988 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CTP synthase 2
EC: 6.3.4.2
UniProt: Q9NRF8
Ligands: ZFY, UTP, GLN, MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E	CTP synthase 2 (EC 6.3.4.2)	protein	497	41% helix, 22% strand	Q9NRF8

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 A, B, C, E
UTP · Uridine 5'-triphosphate · ligand · 4 copies · chains A, B, C, E
GLN · Glutamine · ligand · 4 copies · chains A, B, C, E
MG · Magnesium ion · metal · 4 copies · chains A, B, C, 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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	913	0.86	0.88	100	empty
2	963	0.80	0.82	74	ZFY, UTP, MG
3	797	0.80	0.83	70	MG, ZFY, UTP
4	1017	0.79	0.80	74	ZFY, UTP, MG
5	1129	0.78	0.80	84	MG, ZFY, UTP

Interfaces

6 interfaces between chains.

B–E · 1306 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 1304 Å² buried · 22 hydrogen bonds · protein-protein
C–E · 743 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 742 Å² buried · 4 hydrogen bonds · protein-protein
A–E · 486 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7MII · Human CTPS2 bound to inhibitor T35 · the same entry in another collection · chain E against E, TM-score 1.00
Q9NRF8 · AlphaFold monomer V2.0 prediction for CTP synthase 2 (Q9NRF8) · a predicted model of the same protein · chain C 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 Q9NRF8
Elsewhere: RCSB PDB 7MII · PDBe 7MII · UniProt Q9NRF8

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