Research workbench
Co-crystal structure of nampt dimer with kpt-9274
Analyse Co-crystal structure of nampt dimer with kpt-9274 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NSD
- Type
- protein
- Length
- 932 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
- 96Q, PO4
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 466 | 40% helix, 19% strand | P43490 |
Ligands and binding sites
- 96Q · (~{E})-3-(6-azanylpyridin-3-yl)-~{N}-[[5-[4-[4,4-bis(fluoranyl)piperidin-1-yl]carbonylphenyl]-7-(4-fluorophenyl)-1-benzofuran-2-yl]methyl]prop-2-enamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 14 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 | 863 | 0.81 | 0.83 | 87 | GOL, 96Q, PO4 |
| 2 | 931 | 0.80 | 0.82 | 94 | PO4, GOL, 96Q |
| 3 | 663 | 0.69 | 0.77 | 51 | GOL |
| 4 | 68 | 0.34 | 0.77 | 17 | empty |
| 5 | 65 | 0.33 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 4271 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 5NSD · Co-crystal structure of NAMPT dimer with KPT-9274 · 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 5NSD · PDBe 5NSD · UniProt P43490
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