Research workbench
The crystal structure of human nicotinamide phosphoribosyltransferase (nampt) in complex with N-(4-{(S)-[1-(2-METHYLPROPYL)PIPERIDIN-4- YL]SULFINYL}BENZYL)FURO[2,3-C]PYRIDINE-2-carboxamide inhibitor (compound 21)
Analyse The crystal structure of human nicotinamide phosphoribosyltransferase (nampt)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WQ6
- Type
- protein
- Length
- 939 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
- 3TQ, PO4
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 469 | 42% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 470 | 42% helix, 19% strand | P43490 |
Ligands and binding sites
- 3TQ · N-(4-{(S)-[1-(2-methylpropyl)piperidin-4-yl]sulfinyl}benzyl)furo[2,3-c]pyridine-2-carboxamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.80 | 0.83 | 90 | 3TQ, PO4, EDO |
| 2 | 758 | 0.80 | 0.84 | 83 | PO4, EDO, 3TQ |
| 3 | 648 | 0.72 | 0.79 | 53 | EDO |
| 4 | 87 | 0.36 | 0.76 | 17 | empty |
| 5 | 74 | 0.35 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 4279 Ų buried · 78 hydrogen bonds · protein-protein
Compared structures
- 4WQ6 · The crystal structure of human Nicotinamide phosphoribosyltransferase (NAMPT) in complex… · 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 4WQ6 · PDBe 4WQ6 · UniProt P43490
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