MolNFT v1 · #124562 · protein
Crystal structure of nicotinamide phosphoribosyltransferase (nampt) in complex with inhibitors 37
5KIT: “Crystal structure of nicotinamide phosphoribosyltransferase (nampt) in complex with inhibitors 37”. X-ray diffraction, 2 ligands (6TA, PO4), 7 pockets (best druggability 0.80). MolNFT v1 #124562 on GenesisL1: 3D structure, binding…
- PDB
- 5KIT
- 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
- 6TA, PO4
- Pockets
- 7 · best druggability 0.80
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 | 470 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- 6TA · ~{tert}-butyl (2~{S})-2-[(1,3-dihydropyrrolo[3,4-c]pyridin-2-ylcarbonylamino)methyl]-6-azaspiro[2.5]octane-6-carboxylate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 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 | 847 | 0.80 | 0.83 | 87 | 6TA, PO4, EDO |
| 2 | 727 | 0.79 | 0.83 | 77 | PO4, EDO, 6TA |
| 3 | 755 | 0.73 | 0.79 | 61 | empty |
| 4 | 59 | 0.37 | 0.80 | 21 | empty |
| 5 | 77 | 0.35 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 4269 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 5KIT · Crystal Structure of Nicotinamide Phosphoribosyltransferase (Nampt) in Complex with… · 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 5KIT · PDBe 5KIT · UniProt P43490
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