Research workbench
Selective inhibition of autotaxin is effective in mouse models of liver fibrosis
Analyse Selective inhibition of autotaxin is effective in mouse models of liver fibrosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KXA
- Type
- protein
- Length
- 751 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
- Q13822
- Ligands
- 6Y7, NAG, ZN, CA, PO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 751 | 26% helix, 20% strand | Q13822 |
Ligands and binding sites
- 6Y7 · 3-[6-chloranyl-2-cyclopropyl-1-(1-ethylpyrazol-4-yl)-7-fluoranyl-indol-3-yl]sulfanyl-2-fluoranyl-benzoic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.76 | 0.81 | 65 | ZN, 6Y7, PO4 |
| 2 | 320 | 0.58 | 0.77 | 27 | empty |
| 3 | 124 | 0.53 | 0.82 | 18 | empty |
| 4 | 180 | 0.51 | 0.78 | 28 | empty |
| 5 | 144 | 0.48 | 0.78 | 25 | empty |
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5KXA · Selective Inhibition of Autotaxin is Effective in Mouse Models of Liver Fibrosis · the same entry in another collection · chain A against A, TM-score 1.00
- Q13822 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q13822
- Elsewhere: RCSB PDB 5KXA · PDBe 5KXA · UniProt Q13822
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