MolNFT v1 · #112268 · protein
Structural basis for inhibition of human autotaxin by four novel compounds
4ZGA · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Structural basis for inhibition of human autotaxin by four novel compounds”. X-ray diffraction, 6 ligands (ACD, 4O3, NAG), 7 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 4ZGA
- Type
- protein
- Length
- 740 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
- ACD, 4O3, NAG, CA, ZN, SCN
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 740 | 30% helix, 19% strand | Q13822 |
Ligands and binding sites
- ACD · Arachidonic acid · ligand · chains A
- 4O3 · (11AS)-6-(4-fluorobenzyl)-5,6,11,11A-tetrahydro-1H-imidazo[1',5':1,6]pyrido[3,4-b]indole-1,3(2H)-dione · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- SCN · Thiocyanate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.74 | 0.80 | 70 | EDO, ACD, 4O3 |
| 2 | 358 | 0.66 | 0.80 | 38 | empty |
| 3 | 231 | 0.57 | 0.78 | 41 | SCN |
| 4 | 153 | 0.55 | 0.81 | 29 | empty |
| 5 | 121 | 0.45 | 0.78 | 17 | empty |
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 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 4ZGA · PDBe 4ZGA · UniProt Q13822
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