MolNFT v1 · #185311 · protein
Crystal structure of nampt in complex with compound 10
7PPH · Nicotinamide phosphoribosyltransferase: “Crystal structure of nampt in complex with compound 10”. X-ray diffraction, 2 ligands (7YE, PO4), 4 pockets (best druggability 0.79). MolNFT v1 #185311 on GenesisL1: 3D structure, binding…
- PDB
- 7PPH
- Type
- protein
- Length
- 933 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
- 7YE, PO4
- Pockets
- 4 · 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 | 467 | 41% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 466 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- 7YE · N-[4-[(5R)-6-oxidanylidene-5-quinolin-5-yl-5-(trifluoromethyl)-1,4-dihydropyridazin-3-yl]phenyl]-1, 3-dihydropyrrolo[3,4-c]pyridine-2-carboxamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.79 | 0.84 | 82 | PO4, 7YE, GOL |
| 2 | 739 | 0.78 | 0.82 | 80 | 7YE, PO4, GOL |
| 3 | 546 | 0.69 | 0.78 | 50 | empty |
| 4 | 57 | 0.32 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 4297 Ų buried · 73 hydrogen bonds · protein-protein
Compared structures
- 7PPH · CRYSTAL STRUCTURE OF NAMPT IN COMPLEX WITH Compound 10 · 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 7PPH · PDBe 7PPH · UniProt P43490
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