MolNFT v1 · #99163 · protein
Fragment-based identification of amides derived from trans-2-(pyridin- 3-YL)CYCLOPROPANECARBOXYLIC acid as potent inhibitors of human nicotinamide phosphoribosyltransferase (nampt)
4LVD: “Fragment-based identification of amides derived from trans-2-(pyridin- 3-YL)CYCLOPROPANECARBOXYLIC acid as…”. X-ray diffraction, 2 ligands (1EB, PO4), 7 pockets (best druggability 0.79). MolNFT v1 #99163 on GenesisL1: 3D structure…
- PDB
- 4LVD
- Type
- protein
- Length
- 938 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
- 1EB, PO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 469 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- 1EB · N-(4-nitrophenyl)cyclopropanecarboxamide · ligand · 2 copies · chains B, A
- PO4 · Phosphate ion · ion · 4 copies · chains B, A
- EDO · 1,2-ethanediol · additive · chains B, A
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 | 710 | 0.79 | 0.84 | 81 | PO4, 1EB |
| 2 | 764 | 0.79 | 0.82 | 92 | PO4, EDO, 1EB |
| 3 | 784 | 0.73 | 0.78 | 67 | empty |
| 4 | 55 | 0.34 | 0.78 | 17 | empty |
| 5 | 58 | 0.34 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 4273 Ų buried · 78 hydrogen bonds · protein-protein
Compared structures
- 4LVD · Fragment-based Identification of Amides Derived From… · 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 4LVD · PDBe 4LVD · UniProt P43490
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