MolNFT v1 · #126596 · protein
Novel IMIDAZO[1,2-A]PYRIDINE derivatives with potent AUTOTAXIN/ENPP2 inhibitor activity
5M7M · Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family…: “Novel IMIDAZO[1,2-A]PYRIDINE derivatives with potent AUTOTAXIN/ENPP2 inhibitor activity”. X-ray diffraction, 11 ligands (7HR, MAN, NAG), 10 pockets (best druggability 0.72).…
- PDB
- 5M7M
- Type
- protein
- Length
- 759 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
- 7HR, MAN, NAG, BMA, NI, ZN, K, CL, IOD, SCN, PO4
- Pockets
- 10 · best druggability 0.72
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 | 759 | 29% helix, 19% strand | Q13822 |
Ligands and binding sites
- 7HR · ~{N}-[6-[1-[3-(dimethylamino)propylsulfonyl]piperidin-4-yl]-2-ethyl-imidazo[1,2-a]pyridin-3-yl]-4-(4-fluorophenyl)-~{N}-methyl-1,3-thiazol-2-amine · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- NI · Nickel (II) ion · metal · 7 copies · chains A
- ZN · Zinc ion · metal · 4 copies · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- IOD · Iodide ion · ion · chains A
- SCN · Thiocyanate ion · ion · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.72 | 0.80 | 44 | 7HR |
| 2 | 227 | 0.65 | 0.83 | 33 | empty |
| 3 | 337 | 0.58 | 0.76 | 34 | empty |
| 4 | 206 | 0.56 | 0.79 | 40 | NI |
| 5 | 147 | 0.42 | 0.75 | 28 | empty |
Modifications
Observed in the structure: 14 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5M7M · Novel Imidazo[1,2-a]pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity · 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 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 5M7M · PDBe 5M7M · UniProt Q13822
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