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Human CD73 (ecto 5'-nucleotidase) in complex with compound 12

Analyse Human CD73 (ecto 5'-nucleotidase) in complex with compound 12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JV9
Type: protein
Length: 1,050 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-nucleotidase
EC: 3.1.3.5
UniProt: P21589
Ligands: VPG, NAG, ZN, CA, PO4
Pockets: 7 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-nucleotidase (EC 3.1.3.5)	protein	525	29% helix, 27% strand	P21589

Ligands and binding sites

VPG · 6-chloro-N-[(2-chlorophenyl)methyl]-1-[5-O-(phosphonomethyl)-beta-D-ribofuranosyl]-1H-pyrazolo[3, 4-d]pyrimidin-4-amine · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
ZN · Zinc ion · metal · 4 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B

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

Pockets

7 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	827	0.85	0.87	95	empty
2	629	0.74	0.81	78	VPG
3	656	0.73	0.80	75	VPG
4	53	0.65	0.95	19	empty
5	92	0.60	0.88	29	empty

Interfaces

1 interface between chains.

A–B · 1285 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7JV9 · Human CD73 (ecto 5'-nucleotidase) in complex with compound 12 · the same entry in another collection · chain A against A, TM-score 1.00
P21589 · AlphaFold monomer V2.0 prediction for 5'-nucleotidase (P21589) · 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 P21589
Elsewhere: RCSB PDB 7JV9 · PDBe 7JV9 · UniProt P21589

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