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Crystal structure of nampt in complex with compound 9
Analyse Crystal structure of nampt in complex with compound 9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PPG
- Type
- protein
- Length
- 1,867 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide phosphoribosyltransferase
- EC
- 2.4.2.12
- UniProt
- P43490
- Ligands
- 7YX, PO4
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 467 | 41% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 466 | 42% helix, 19% strand | P43490 |
Ligands and binding sites
- 7YX · N-[4-[(4R)-1-cyclopentyl-4-methyl-6-oxidanylidene-4,5-dihydropyridazin-3-yl]phenyl]-1,3-dihydropyrrolo[3,4-c]pyridine-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.80 | 0.83 | 79 | PO4, EDO, 7YX |
| 2 | 731 | 0.79 | 0.84 | 78 | PO4, 7YX |
| 3 | 739 | 0.79 | 0.83 | 79 | PO4, EDO, 7YX |
| 4 | 740 | 0.79 | 0.83 | 82 | PO4, 7YX, EDO |
| 5 | 515 | 0.69 | 0.78 | 51 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4297 Ų buried · 79 hydrogen bonds · protein-protein
- C–D · 4291 Ų buried · 74 hydrogen bonds · protein-protein
- B–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7PPG · Crystal structure of nampt in complex with compound 9 · 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 7PPG · PDBe 7PPG · UniProt P43490
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