MolNFT v1 · #125047 · protein
Selective inhibition of autotaxin is effective in mouse models of liver fibrosis
5KXA · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Selective inhibition of autotaxin is effective in mouse models of liver fibrosis”. X-ray diffraction, 5 ligands (6Y7, NAG, ZN), 8 pockets (best druggability 0.76). MolNFT v1…
- 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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