MolNFT v1 · #171558 · protein
Human ecto-5'-nucleotidase (CD73) in complex with aopcp derivative A830 (compound 16 in publication) in the closed form (crystal form III)
6Z9B: “Human ecto-5'-nucleotidase (CD73) in complex with aopcp derivative A830 (compound 16 in publication) in the…”. X-ray diffraction, 3 ligands (QCQ, ZN, CA), 5 pockets (best druggability 0.76). MolNFT v1 #171558 on GenesisL1: 3D…
- PDB
- 6Z9B
- Type
- protein
- Length
- 521 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-nucleotidase
- EC
- 3.1.3.5
- UniProt
- P21589
- Ligands
- QCQ, ZN, CA
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase (EC 3.1.3.5) | protein | 521 | 31% helix, 26% strand | P21589 |
Ligands and binding sites
- QCQ · [[(2~{R},3~{R},4~{S},5~{R})-5-[2-chloranyl-6-[(phenylmethyl)amino]purin-9-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.76 | 0.80 | 79 | QCQ |
| 2 | 112 | 0.64 | 0.89 | 32 | empty |
| 3 | 72 | 0.37 | 0.78 | 19 | empty |
| 4 | 59 | 0.29 | 0.75 | 15 | empty |
| 5 | 61 | 0.29 | 0.74 | 22 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6Z9B · Human Ecto-5'-nucleotidase (CD73) in complex with AOPCP derivative A830 (compound 16 in… · 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 A against A, TM-score 0.97
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 6Z9B · PDBe 6Z9B · UniProt P21589
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