MolNFT v1 · #135561 · protein
Crystal structure of human nampt with a-1326133
5U2N · Nicotinamide phosphoribosyltransferase: “Crystal structure of human nampt with a-1326133”. X-ray diffraction, 2 ligands (7TA, SO4), 5 pockets (best druggability 0.80). MolNFT v1 #135561 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5U2N
- Type
- protein
- Length
- 929 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
- 7TA, SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 465 | 41% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 464 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- 7TA · N-{4-[1-(2-methylpropanoyl)piperidin-4-yl]phenyl}-2H-pyrrolo[3,4-c]pyridine-2-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 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 | 726 | 0.80 | 0.84 | 79 | SO4, 7TA |
| 2 | 709 | 0.79 | 0.83 | 84 | SO4, 7TA |
| 3 | 556 | 0.69 | 0.78 | 48 | empty |
| 4 | 52 | 0.35 | 0.80 | 19 | empty |
| 5 | 67 | 0.31 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 4288 Ų buried · 78 hydrogen bonds · protein-protein
Compared structures
- 5U2N · Crystal structure of human NAMPT with A-1326133 · 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 5U2N · PDBe 5U2N · UniProt P43490
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