Research workbench
Crystal structure of human nampt with fragment 5: (3E)-3- [(PHENYLAMINO)METHYLIDENE]OXAN-2-one
Analyse Crystal structure of human nampt with fragment 5: (3E)-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WI1
- 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
- AOY, SO4
- Pockets
- 4 · 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
- AOY · (3E)-3-[(phenylamino)methylidene]oxan-2-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 743 | 0.79 | 0.83 | 86 | AOY, SO4 |
| 2 | 675 | 0.78 | 0.83 | 77 | SO4, AOY |
| 3 | 545 | 0.69 | 0.78 | 47 | empty |
| 4 | 62 | 0.32 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 4322 Ų buried · 83 hydrogen bonds · protein-protein
Compared structures
- 5WI1 · Crystal structure of human NAMPT with fragment 5… · 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 5WI1 · PDBe 5WI1 · UniProt P43490
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