Research workbench
Human ecto-5'-nucleotidase (CD73) in complex with A1618 (compound 1B in publication) in the closed state in crystal form III
Analyse Human ecto-5'-nucleotidase (CD73) in complex with A1618 (compound 1B in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XUQ
- Type
- protein
- Length
- 514 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
- O1T, ZN, CA
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase (EC 3.1.3.5) | protein | 514 | 31% helix, 25% strand | P21589 |
Ligands and binding sites
- O1T · [[(2~{R},3~{S},4~{R},5~{R})-5-[6-chloranyl-4-[[(1~{S})-1-(4-fluorophenyl)ethyl]amino]pyrazolo[3,4-b]pyridin-1-yl]-3,4-bis(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 | 782 | 0.75 | 0.80 | 78 | ZN, O1T |
| 2 | 77 | 0.61 | 0.90 | 23 | empty |
| 3 | 61 | 0.35 | 0.78 | 17 | empty |
| 4 | 54 | 0.27 | 0.74 | 15 | empty |
| 5 | 56 | 0.25 | 0.72 | 20 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6XUQ · Human Ecto-5'-nucleotidase (CD73) in complex with A1618 (compound 1b in publication) 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 0.98
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 6XUQ · PDBe 6XUQ · UniProt P21589
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