MolNFT v1 · #133745 · protein
Autotaxin, 4-[3-oxo-3-(2-oxo-2,3-dihydro-benzooxazol-6-yl)-propyl]- piperazine-1-carboxylic acid 3,5-dichloro-benzyl ester, 1.90A, P212121, RFREE=19.1%
5S9L · Isoform 2 of ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERAS…: “Autotaxin, 4-[3-oxo-3-(2-oxo-2,3-dihydro-benzooxazol-6-yl)-propyl]- piperazine-1-carboxylic acid…”. X-ray diffraction, 7 ligands (6ZO, MAN, NAG), 14 pockets (best…
- PDB
- 5S9L
- Type
- protein
- Length
- 805 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
- 6ZO, MAN, NAG, CA, K, ZN, NA
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 18% 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 | 805 | 31% helix, 18% strand | Q64610 |
Ligands and binding sites
- 6ZO · (3,5-dichlorophenyl)methyl 4-[3-oxo-3-(2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)propyl]piperazine-1-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
- CA · Calcium ion · metal · 2 copies · chains A
- K · Potassium ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- ACT · Acetate ion · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.77 | 0.79 | 86 | ACT, 6ZO, ZN |
| 2 | 282 | 0.60 | 0.79 | 29 | ACT |
| 3 | 248 | 0.59 | 0.79 | 27 | empty |
| 4 | 281 | 0.58 | 0.78 | 28 | empty |
| 5 | 201 | 0.51 | 0.77 | 34 | empty |
Modifications
Observed in the structure: 15 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5S9L · AUTOTAXIN, 4-[3-Oxo-3-(2-oxo-2,3-dihydro-benzooxazol-6-yl)-propyl]-piperazine-1-carboxylic… · 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 0.99
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 Q64610
- Elsewhere: RCSB PDB 5S9L · PDBe 5S9L · UniProt Q64610
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