Research workbench
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
- 4N9D
- Type
- protein
- Length
- 939 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
- 2HJ, PO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 469 | 41% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 470 | 42% helix, 19% strand | P43490 |
Ligands and binding sites
- 2HJ · 4-({[(4-tert-butylphenyl)sulfonyl]amino}methyl)-N-(pyridin-3-yl)benzamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.80 | 0.83 | 88 | 2HJ, EDO, PO4 |
| 2 | 716 | 0.79 | 0.84 | 81 | PO4, EDO, 2HJ |
| 3 | 648 | 0.71 | 0.79 | 54 | empty |
| 4 | 53 | 0.38 | 0.80 | 16 | empty |
| 5 | 78 | 0.37 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 4242 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 4N9D · Fragment-based Design of 3-Aminopyridine-derived Amides as Potent Inhibitors of Human… · the same entry in another collection · chain B against B, 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 4N9D · PDBe 4N9D · UniProt P43490
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