MolNFT v1 · #147218 · protein
Nampt co-crystal with inhibitor compound 2
6E68 · Nicotinamide phosphoribosyltransferase: “Nampt co-crystal with inhibitor compound 2”. X-ray diffraction, 2 ligands (HVM, PO4), 7 pockets (best druggability 0.79). MolNFT v1 #147218 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6E68
- Type
- protein
- Length
- 940 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
- HVM, PO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 471 | 42% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 469 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- HVM · (2E)-N-{4-[1-(3-aminobenzene-1-carbonyl)piperidin-4-yl]butyl}-3-(pyridin-3-yl)prop-2-enamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 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 | 758 | 0.79 | 0.83 | 83 | HVM, PO4 |
| 2 | 729 | 0.79 | 0.83 | 79 | PO4, HVM |
| 3 | 738 | 0.74 | 0.79 | 61 | empty |
| 4 | 76 | 0.36 | 0.77 | 15 | empty |
| 5 | 60 | 0.34 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 4267 Ų buried · 80 hydrogen bonds · protein-protein
Compared structures
- 6E68 · NAMPT co-crystal with inhibitor compound 2 · 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 6E68 · PDBe 6E68 · UniProt P43490
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