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
- 4N9C
- Type
- protein
- Length
- 939 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.751
- Source
- Homo sapiens
- Molecule
- Nicotinamide phosphoribosyltransferase
- EC
- 2.4.2.12
- UniProt
- P43490
- Ligands
- 2ZM, PO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.751 · 2 distinct chains · 41% 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 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- 2ZM · 5-nitro-1H-benzimidazole · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.80 | 0.83 | 90 | 2ZM, PO4 |
| 2 | 381 | 0.75 | 0.86 | 50 | PO4 |
| 3 | 645 | 0.72 | 0.79 | 48 | empty |
| 4 | 342 | 0.66 | 0.81 | 39 | 2ZM |
| 5 | 89 | 0.37 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 4234 Ų buried · 74 hydrogen bonds · protein-protein
Compared structures
- 4N9C · 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
- P43490 · AlphaFold monomer V2.0 prediction for nicotinamide phosphoribosyltransferase (P43490) · 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 P43490
- Elsewhere: RCSB PDB 4N9C · PDBe 4N9C · UniProt P43490
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