Research workbench
Crystal structure of visfatin in complex with SAR154782.
Analyse Crystal structure of visfatin in complex with SAR154782. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LX3
- Type
- protein
- Length
- 926 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
- 7A1
- Pockets
- 6 · best druggability 0.80
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 | 463 | 42% helix, 19% strand | P43490 |
Ligands and binding sites
- 7A1 · 6-[4-[(6-azanylpyridin-3-yl)methylcarbamoylamino]-3-fluoranyl-phenyl]-2-(ethylamino)-~{N}-(2-piperidin-1-ylethyl)pyridine-3-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.80 | 0.83 | 83 | 7A1 |
| 2 | 775 | 0.80 | 0.83 | 89 | 7A1 |
| 3 | 587 | 0.70 | 0.78 | 50 | empty |
| 4 | 63 | 0.32 | 0.76 | 14 | empty |
| 5 | 51 | 0.30 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 4266 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 5LX3 · Crystal structure of visfatin in complex with SAR154782. · 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 5LX3 · PDBe 5LX3 · UniProt P43490
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