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Human cytosolic 5'-nucleotidase II in complex with N-(9H-purin-6-yl)- 3-(3-pyrrol-1-YLPHENYL)BENZAMIDE

Analyse Human cytosolic 5'-nucleotidase II in complex with N-(9H-purin-6-yl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CR7
Type: protein
Length: 913 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytosolic purine 5'-nucleotidase
EC: 3.1.3.5
UniProt: P49902
Ligands: 5WO, MG, PO4
Pockets: 9 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytosolic purine 5'-nucleotidase (EC 3.1.3.5)	protein	459	40% helix, 19% strand	P49902
B	Cytosolic purine 5'-nucleotidase (EC 3.1.3.5)	protein	454	38% helix, 18% strand	P49902

Ligands and binding sites

5WO · ~{N}-(7~{H}-purin-6-yl)-3-(3-pyrrol-1-ylphenyl) benzamide · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 5 copies · chains A, B
GOL · Glycerol · additive · 11 copies · chains A, B
ACT · Acetate ion · additive · 10 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1094	0.83	0.84	99	PO4, GOL
2	997	0.83	0.84	90	ACT, PO4, GOL
3	425	0.77	0.86	50	empty
4	290	0.66	0.82	29	PO4, MG
5	387	0.65	0.79	48	5WO, GOL

Interfaces

1 interface between chains.

A–B · 4076 Å² buried · 58 hydrogen bonds · protein-protein

Compared structures

5CR7 · Human cytosolic 5'-nucleotidase II in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
P49902 · AlphaFold monomer V2.0 prediction for cytosolic purine 5'-nucleotidase (P49902) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P49902
Elsewhere: RCSB PDB 5CR7 · PDBe 5CR7 · UniProt P49902

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