MolNFT v1 · #115686 · protein
Human cytosolic 5'-nucleotidase II in complex with 3-(3-imidazol-1- ylphenyl)-N-(9H-purin-6-YL)BENZAMIDE
5CQZ · Cytosolic purine 5'-nucleotidase: “Human cytosolic 5'-nucleotidase II in complex with 3-(3-imidazol-1- ylphenyl)-N-(9H-purin-6-YL)BENZAMIDE”. X-ray diffraction, 3 ligands (53O, MG, SO4), 8 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 5CQZ
- Type
- protein
- Length
- 919 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
- 53O, MG, SO4
- Pockets
- 8 · 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 | 466 | 39% helix, 18% strand | P49902 |
| B | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 453 | 40% helix, 19% strand | P49902 |
Ligands and binding sites
- 53O · 1-(biphenyl-3-yl)-1H-imidazole · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.83 | 0.84 | 95 | GOL, 53O |
| 2 | 739 | 0.81 | 0.85 | 76 | MG |
| 3 | 652 | 0.77 | 0.83 | 67 | GOL, 53O |
| 4 | 357 | 0.63 | 0.79 | 51 | SO4, MG |
| 5 | 323 | 0.63 | 0.80 | 34 | SO4, MG |
Interfaces
1 interface between chains.
- A–B · 4069 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
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 5CQZ · PDBe 5CQZ · UniProt P49902
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