MolNFT v1 · #136324 · protein
Crystal structure of human nampt with isoindoline urea inhibitor compound 53
5UPF · Nicotinamide phosphoribosyltransferase: “Crystal structure of human nampt with isoindoline urea inhibitor compound 53”. X-ray diffraction, 1 ligand (8HV), 5 pockets (best druggability 0.79). MolNFT v1 #136324 on GenesisL1: 3D…
- PDB
- 5UPF
- Type
- protein
- Length
- 928 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
- 8HV
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 464 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- 8HV · 5-fluoro-N-{4-[1-(2-hydroxy-2-methylpropanoyl)piperidin-4-yl]phenyl}-2H-isoindole-2-carboxamide · 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 | 714 | 0.79 | 0.84 | 78 | 8HV |
| 2 | 738 | 0.79 | 0.83 | 87 | 8HV |
| 3 | 543 | 0.69 | 0.78 | 47 | empty |
| 4 | 50 | 0.30 | 0.77 | 18 | empty |
| 5 | 52 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 4309 Ų buried · 82 hydrogen bonds · protein-protein
Compared structures
- 5UPF · Crystal structure of human NAMPT with isoindoline urea inhibitor compound 53 · 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 5UPF · PDBe 5UPF · UniProt P43490
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