MolNFT v1 · #133746 · protein
Autotaxin, (3,5-DICHLOROPHENYL)METHYL (3AS,8AR)-2-(1H-benzotriazole-5- carbonyl)-1,3,3A,4,5,7,8,8A-OCTAHYDROPYRROLO[3,4-D]AZEPINE-6- carboxylate, 1.80A, P212121, RFREE=21.1%
5S9M · Isoform 2 of ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERAS…: “Autotaxin, (3,5-DICHLOROPHENYL)METHYL (3AS,8AR)-2-(1H-benzotriazole-5…”. X-ray diffraction, 8 ligands (YV1, MAN, NAG), 12 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5S9M
- Type
- protein
- Length
- 809 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
- YV1, MAN, NAG, BMA, CA, ZN, NA, CL
- Pockets
- 12 · best druggability 0.80
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 | 809 | 30% helix, 19% strand | Q64610 |
Ligands and binding sites
- YV1 · (3,5-dichlorophenyl)methyl (3aR,8aS)-2-(1H-benzotriazole-5-carbonyl)octahydropyrrolo[3,4-d]azepine-6(1H)-carboxylate · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · 6 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 · 3 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 3 copies · chains A
- PG4 · Tetraethylene glycol · additive · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.80 | 0.81 | 82 | YV1, ACT |
| 2 | 485 | 0.66 | 0.78 | 58 | ACT |
| 3 | 289 | 0.59 | 0.78 | 35 | empty |
| 4 | 242 | 0.58 | 0.79 | 25 | empty |
| 5 | 246 | 0.54 | 0.77 | 49 | empty |
Modifications
Observed in the structure: 15 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5S9M · AUTOTAXIN, (3,5-dichlorophenyl)methyl (3aS,8aR)-2-(1H-benzotriazole-5-carbonyl)-1,3,3a,4,5… · 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 5S9M · PDBe 5S9M · UniProt Q64610
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