Research workbench
Structural basis for inhibition of human autotaxin by four novel compounds
Analyse Structural basis for inhibition of human autotaxin by four novel compounds in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZG7
- Type
- protein
- Length
- 776 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
- 4O0, NKN, NAG, ZN, NA, CA, CL
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 776 | 29% helix, 19% strand | Q13822 |
Ligands and binding sites
- 4O0 · 3-({6-chloro-7-fluoro-2-methyl-1-[2-oxo-2-(spiro[cyclopropane-1,3'-indol]-1'(2'H)-yl)ethyl]-1H-indol-3-yl}sulfanyl)-2-fluorobenzoic acid · ligand · chains A
- NKN · (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.76 | 0.81 | 62 | 4O0, NKN, GOL, CL |
| 2 | 371 | 0.66 | 0.80 | 43 | GOL |
| 3 | 296 | 0.60 | 0.78 | 38 | empty |
| 4 | 162 | 0.51 | 0.78 | 29 | empty |
| 5 | 73 | 0.48 | 0.83 | 14 | empty |
Modifications
Observed in the structure: 15 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 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 Q13822
- Elsewhere: RCSB PDB 4ZG7 · PDBe 4ZG7 · UniProt Q13822
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