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Fragment-based design of 3-aminopyridine-derived amides as potent inhibitors of human nicotinamide phosphoribosyltransferase (nampt)
Analyse Fragment-based design of 3-aminopyridine-derived amides as potent inhibitors of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N9E
- Type
- protein
- Length
- 940 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
- 2HL, PO4
- Pockets
- 6 · best druggability 0.79
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 | 471 | 42% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 469 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- 2HL · 1-[(1-benzoylpiperidin-4-yl)methyl]-N-(pyridin-3-yl)-1H-benzimidazole-5-carboxamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.79 | 0.83 | 85 | 2HL, EDO, DTT, PO4 |
| 2 | 733 | 0.79 | 0.83 | 77 | PO4, EDO, DTT, 2HL |
| 3 | 720 | 0.74 | 0.79 | 55 | EDO |
| 4 | 59 | 0.35 | 0.79 | 22 | empty |
| 5 | 80 | 0.35 | 0.76 | 14 | EDO |
Interfaces
1 interface between chains.
- A–B · 4270 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 4N9E · Fragment-based Design of 3-Aminopyridine-derived Amides as Potent Inhibitors of Human… · 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 4N9E · PDBe 4N9E · UniProt P43490
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