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
- 4LVF
- 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
- 20P, PO4
- Pockets
- 7 · 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
- 20P · (1S,2S)-2-phenyl-N-(pyridin-4-yl)cyclopropanecarboxamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 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 | 738 | 0.80 | 0.84 | 83 | PO4, EDO, 20P |
| 2 | 775 | 0.79 | 0.83 | 87 | 20P, EDO, PO4 |
| 3 | 693 | 0.73 | 0.79 | 58 | empty |
| 4 | 100 | 0.39 | 0.76 | 23 | empty |
| 5 | 84 | 0.36 | 0.76 | 19 | EDO |
Interfaces
1 interface between chains.
- A–B · 4218 Ų buried · 75 hydrogen bonds · protein-protein
Compared structures
- 4LVF · 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 4LVF · PDBe 4LVF · UniProt P43490
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