MolNFT v1 · #37678 · protein
Crystal structure of VISFATIN/PRE-B cell colony enhancing factor 1/NICOTINAMIDE phosphoribosyltransferase in complex with the specific inhibitor fk-866
2G97: “Crystal structure of VISFATIN/PRE-B cell colony enhancing factor 1/NICOTINAMIDE phosphoribosyltransferase in…”. X-ray diffraction, 1 ligand (DGB), 5 pockets (best druggability 0.78). MolNFT v1 #37678 on GenesisL1: 3D structure…
- PDB
- 2G97
- 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
- DGB
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 463 | 39% helix, 21% strand | Q80Z29 |
Ligands and binding sites
- DGB · (2E)-N-{4-[1-(benzenecarbonyl)piperidin-4-yl]butyl}-3-(pyridin-3-yl)prop-2-enamide · 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 | 782 | 0.78 | 0.82 | 92 | DGB |
| 2 | 608 | 0.77 | 0.83 | 77 | DGB |
| 3 | 469 | 0.67 | 0.78 | 44 | empty |
| 4 | 55 | 0.29 | 0.75 | 18 | empty |
| 5 | 53 | 0.28 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 4288 Ų buried · 95 hydrogen bonds · protein-protein
Compared structures
- 2G97 · Crystal Structure of Visfatin/Pre-B Cell Colony Enhancing Factor 1/Nicotinamide… · 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 2G97 · PDBe 2G97 · UniProt Q80Z29
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