MolNFT v1 · #64609 · protein
Crystal structure of rattus norvegicus VISFATIN/PBEF/NAMPT in complex with an FK866-based inhibitor
3G8E · Nicotinamide phosphoribosyltransferase: “Crystal structure of rattus norvegicus VISFATIN/PBEF/NAMPT in complex with an FK866-based inhibitor”. X-ray diffraction, 1 ligand (IS1), 5 pockets (best druggability 0.80). MolNFT v1 #64609…
- PDB
- 3G8E
- Type
- protein
- Length
- 926 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide phosphoribosyltransferase
- EC
- 2.4.2.12
- UniProt
- Q80Z29
- Ligands
- IS1
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 463 | 36% helix, 19% strand | Q80Z29 |
Ligands and binding sites
- IS1 · 3-[(1E)-3-oxo-3-({4-[1-(phenylcarbonyl)piperidin-4-yl]butyl}amino)prop-1-en-1-yl]-1-beta-D-ribofuranosylpyridinium · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.80 | 0.84 | 85 | IS1 |
| 2 | 698 | 0.79 | 0.84 | 76 | IS1 |
| 3 | 430 | 0.64 | 0.77 | 44 | empty |
| 4 | 86 | 0.39 | 0.78 | 19 | empty |
| 5 | 73 | 0.32 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 4203 Ų buried · 73 hydrogen bonds · protein-protein
Compared structures
- 3G8E · Crystal Structure of Rattus norvegicus Visfatin/PBEF/Nampt in Complex with an FK866-based… · the same entry in another collection · chain A against A, TM-score 1.00
- Q80Z29 · AlphaFold monomer V2.0 prediction for nicotinamide phosphoribosyltransferase (Q80Z29) · a predicted model of the same protein · 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 Q80Z29
- Elsewhere: RCSB PDB 3G8E · PDBe 3G8E · UniProt Q80Z29
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