Research workbench
Structure-based discovery of novel amide-containing nicotinamide phosphoribosyltransferase (nampt) inhibitors
Analyse Structure-based discovery of novel amide-containing nicotinamide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KFO
- Type
- protein
- Length
- 942 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide phosphoribosyltransferase
- EC
- 2.4.2.12
- UniProt
- P43490
- Ligands
- 1QS, PO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 472 | 41% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 470 | 40% helix, 19% strand | P43490 |
Ligands and binding sites
- 1QS · N-{4-[(3,5-difluorophenyl)sulfonyl]benzyl}imidazo[1,2-a]pyridine-6-carboxamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.80 | 0.83 | 82 | PO4, EDO, 1QS |
| 2 | 788 | 0.80 | 0.83 | 83 | 1QS, PO4, EDO |
| 3 | 698 | 0.74 | 0.80 | 60 | empty |
| 4 | 65 | 0.37 | 0.79 | 23 | empty |
| 5 | 82 | 0.36 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 4299 Ų buried · 78 hydrogen bonds · protein-protein
Compared structures
- 4KFO · Structure-Based Discovery of Novel Amide-Containing Nicotinamide… · the same entry in another collection · 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 P43490
- Elsewhere: RCSB PDB 4KFO · PDBe 4KFO · UniProt P43490
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