MolNFT v1 · #135560 · protein
Crystal structure of human nampt with a-1293201
5U2M · Nicotinamide phosphoribosyltransferase: “Crystal structure of human nampt with a-1293201”. X-ray diffraction, 2 ligands (7T7, SO4), 3 pockets (best druggability 0.80). MolNFT v1 #135560 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5U2M
- 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
- 7T7, SO4
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 464 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- 7T7 · N-[4-({[(3S)-oxolan-3-yl]methyl}carbamoyl)phenyl]-1,3-dihydro-2H-isoindole-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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.80 | 0.84 | 81 | SO4, 7T7 |
| 2 | 658 | 0.78 | 0.84 | 76 | 7T7, SO4 |
| 3 | 536 | 0.69 | 0.79 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 4308 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 5U2M · Crystal structure of human NAMPT with A-1293201 · 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 5U2M · PDBe 5U2M · UniProt P43490
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