MolNFT v1 · #133747 · protein
Autotaxin, [4-(TRIFLUOROMETHOXY)PHENYL]METHYL (3AS,6AS)-2-(1H- benzotriazole-5-carbonyl)-1,3,3A,4,6,6A-HEXAHYDROPYRROLO[3,4- C]PYRROLE-5-carboxylate, 1.80A, P212121, RFREE=23.3%
5S9N · Isoform 2 of ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERAS…: “Autotaxin, [4-(TRIFLUOROMETHOXY)PHENYL]METHYL (3AS,6AS)-2-(1H…”. X-ray diffraction, 8 ligands (YVS, MAN, NAG), 12 pockets (best druggability 0.76). MolNFT v1 #133747 on…
- PDB
- 5S9N
- Type
- protein
- Length
- 808 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2
- EC
- 3.1.4.39
- UniProt
- Q64610
- Ligands
- YVS, MAN, NAG, BMA, CA, ZN, NA, CL
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 808 | 30% helix, 19% strand | Q64610 |
Ligands and binding sites
- YVS · [4-(trifluoromethoxy)phenyl]methyl (3aR,6aS)-5-(1H-benzotriazole-5-carbonyl)hexahydropyrrolo[3,4-c]pyrrole-2(1H)-carboxylate · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.76 | 0.78 | 83 | YVS, ZN, CL |
| 2 | 304 | 0.59 | 0.78 | 33 | empty |
| 3 | 269 | 0.59 | 0.79 | 27 | empty |
| 4 | 239 | 0.56 | 0.78 | 32 | empty |
| 5 | 189 | 0.51 | 0.77 | 37 | empty |
Modifications
Observed in the structure: 15 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5S9N · AUTOTAXIN, [4-(trifluoromethoxy)phenyl]methyl (3aS,6aS)-2-(1H-benzotriazole-5-carbonyl)-1… · the same entry in another collection · chain A against A, TM-score 1.00
- Q64610 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · 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 Q64610
- Elsewhere: RCSB PDB 5S9N · PDBe 5S9N · UniProt Q64610
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