MolNFT v1 · #99160 · protein
Fragment-based identification of amides derived from trans-2-(pyridin- 3-YL)CYCLOPROPANECARBOXYLIC acid as potent inhibitors of human nicotinamide phosphoribosyltransferase (nampt)
4LVA: “Fragment-based identification of amides derived from trans-2-(pyridin- 3-YL)CYCLOPROPANECARBOXYLIC acid as…”. X-ray diffraction, 2 ligands (20M, PO4), 7 pockets (best druggability 0.79). MolNFT v1 #99160 on GenesisL1: 3D structure…
- PDB
- 4LVA
- 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
- 20M, PO4
- Pockets
- 7 · best druggability 0.79
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
- 20M · N-(4-{[4-(pyrrolidin-1-yl)piperidin-1-yl]sulfonyl}benzyl)-2H-pyrido[4,3-e][1,2,4]thiadiazin-3-amine 1,1-dioxide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 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 | 790 | 0.79 | 0.83 | 83 | 20M, PO4, EDO |
| 2 | 738 | 0.79 | 0.83 | 79 | PO4, EDO, 20M |
| 3 | 674 | 0.73 | 0.79 | 59 | EDO |
| 4 | 94 | 0.39 | 0.77 | 18 | empty |
| 5 | 98 | 0.38 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 4233 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 4LVA · 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 4LVA · PDBe 4LVA · UniProt P43490
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