Research workbench
Fragment-based identification of amides derived from trans-2-(pyridin- 3-YL)CYCLOPROPANECARBOXYLIC acid as potent inhibitors of human nicotinamide phosphoribosyltransferase (nampt)
Analyse Fragment-based identification of amides derived from trans-2-(pyridin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LVB
- Type
- protein
- Length
- 941 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
- 20N, 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 | 470 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- 20N · N-[4-(acetylamino)phenyl]cyclopropanecarboxamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 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 | 776 | 0.79 | 0.83 | 89 | 20N, PO4, EDO |
| 2 | 747 | 0.79 | 0.83 | 81 | PO4, 20N, EDO |
| 3 | 700 | 0.73 | 0.79 | 63 | empty |
| 4 | 72 | 0.38 | 0.78 | 14 | empty |
| 5 | 55 | 0.32 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 4215 Ų buried · 72 hydrogen bonds · protein-protein
Compared structures
- 4LVB · Fragment-based Identification of Amides Derived From… · 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 4LVB · PDBe 4LVB · UniProt P43490
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