Research workbench
Crystal structure of human nampt complexed with benzamide and phosphoribosyl pyrophosphate
Analyse Crystal structure of human nampt complexed with benzamide and phosphoribosyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DKJ
- Type
- protein
- Length
- 928 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
- PRP, UNU
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 464 | 42% helix, 19% strand | P43490 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- UNU · Benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.79 | 0.84 | 76 | PRP, UNU |
| 2 | 734 | 0.79 | 0.84 | 85 | PRP, UNU |
| 3 | 585 | 0.70 | 0.78 | 56 | empty |
| 4 | 64 | 0.32 | 0.76 | 18 | empty |
| 5 | 64 | 0.29 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4275 Ų buried · 75 hydrogen bonds · protein-protein
Compared structures
- 3DKJ · Crystal structure of human NAMPT complexed with benzamide and phosphoribosyl pyrophosphate · 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 3DKJ · PDBe 3DKJ · UniProt P43490
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