MolNFT v1 · #165461 · protein
Human CD73 (ecto 5'-nucleotidase) in complex with PSB12646 (an aopcp derivative, compound 20 in publication) in the closed state
6TWA: “Human CD73 (ecto 5'-nucleotidase) in complex with PSB12646 (an aopcp derivative, compound 20 in publication)…”. X-ray diffraction, 3 ligands (O02, ZN, CA), 4 pockets (best druggability 0.74). MolNFT v1 #165461 on GenesisL1: 3D…
- PDB
- 6TWA
- Type
- protein
- Length
- 519 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
- O02, ZN, CA
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase (EC 3.1.3.5) | protein | 519 | 30% helix, 27% strand | P21589 |
Ligands and binding sites
- O02 · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-diazanyl-purin-9-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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.74 | 0.80 | 83 | O02 |
| 2 | 93 | 0.65 | 0.91 | 26 | empty |
| 3 | 59 | 0.29 | 0.74 | 15 | empty |
| 4 | 56 | 0.25 | 0.72 | 21 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6TWA · Human CD73 (ecto 5'-nucleotidase) in complex with PSB12646 (an AOPCP derivative, compound… · 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 6TWA · PDBe 6TWA · UniProt P21589
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