MolNFT v1 · #122384 · protein
Crystal structure of AUTOTAXIN/ENPP2 with a covalent fragment
5INH · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Crystal structure of AUTOTAXIN/ENPP2 with a covalent fragment”. X-ray diffraction, 6 ligands (6C1, NAG, MAN), 12 pockets (best druggability 0.77). MolNFT v1 #122384 on…
- PDB
- 5INH
- Type
- protein
- Length
- 780 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2
- EC
- 3.1.4.39
- UniProt
- Q9R1E6
- Ligands
- 6C1, NAG, MAN, BMA, ZN, CA
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 780 | 29% helix, 20% strand | Q9R1E6 |
Ligands and binding sites
- 6C1 · {2-[(3-chlorophenyl)methoxy]phenyl}boronic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.77 | 0.79 | 89 | ACT, 6C1 |
| 2 | 448 | 0.69 | 0.80 | 46 | empty |
| 3 | 257 | 0.58 | 0.79 | 29 | empty |
| 4 | 129 | 0.51 | 0.80 | 17 | empty |
| 5 | 140 | 0.47 | 0.78 | 31 | empty |
Modifications
Observed in the structure: 15 disulfide, 3 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 5INH · Crystal structure of Autotaxin/ENPP2 with a covalent fragment · the same entry in another collection · chain A against A, TM-score 1.00
- Q9R1E6 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9R1E6
- Elsewhere: RCSB PDB 5INH · PDBe 5INH · UniProt Q9R1E6
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