MolNFT v1 · #101762 · protein
The crystal structure of a mutant nampt (S165F) in complex with gne- 618
4O15 · Nicotinamide phosphoribosyltransferase: “The crystal structure of a mutant nampt (S165F) in complex with gne- 618”. X-ray diffraction, 2 ligands (2P1, PO4), 6 pockets (best druggability 0.86). MolNFT v1 #101762 on GenesisL1: 3D…
- PDB
- 4O15
- Type
- protein
- Length
- 931 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
- 2P1, PO4
- Pockets
- 6 · best druggability 0.86
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 | 465 | 42% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 466 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- 2P1 · N-(4-{[3-(trifluoromethyl)phenyl]sulfonyl}benzyl)-2H-pyrazolo[3,4-b]pyridine-5-carboxamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 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 | 650 | 0.86 | 0.91 | 95 | PO4, EDO, 2P1 |
| 2 | 286 | 0.79 | 0.90 | 49 | 2P1, PO4 |
| 3 | 729 | 0.73 | 0.79 | 62 | empty |
| 4 | 85 | 0.39 | 0.78 | 16 | empty |
| 5 | 86 | 0.37 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 4293 Ų buried · 77 hydrogen bonds · protein-protein
Compared structures
- 4O15 · The crystal structure of a mutant NAMPT (S165F) in complex with GNE-618 · 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 4O15 · PDBe 4O15 · UniProt P43490
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