Research workbench
Crystal structure of nampt in complex with compound 8
Analyse Crystal structure of nampt in complex with compound 8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PPF
- Type
- protein
- Length
- 934 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
- 7YT, PO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 467 | 40% helix, 19% strand | P43490 |
Ligands and binding sites
- 7YT · N-[4-[(4R)-1,4-dimethyl-6-oxidanylidene-4,5-dihydropyridazin-3-yl]phenyl]-5,7-dihydropyrrolo[3,4-b]pyridine-6-carboxamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.80 | 0.83 | 88 | 7YT, PO4 |
| 2 | 733 | 0.80 | 0.84 | 73 | PO4, EDO, 7YT |
| 3 | 536 | 0.68 | 0.78 | 46 | empty |
| 4 | 63 | 0.33 | 0.77 | 18 | empty |
| 5 | 72 | 0.32 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4284 Ų buried · 78 hydrogen bonds · protein-protein
Compared structures
- 7PPF · Crystal structure of nampt in complex with compound 8 · 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 7PPF · PDBe 7PPF · UniProt P43490
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