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Crystal structure of visfatin in complex with SAR154782-rp.
Analyse Crystal structure of visfatin in complex with SAR154782-rp. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LX5
- Type
- protein
- Length
- 926 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.88
- Source
- Homo sapiens
- Molecule
- Nicotinamide phosphoribosyltransferase
- EC
- 2.4.2.12
- UniProt
- P43490
- Ligands
- 7A0, DPO
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.88 · 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 | 463 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- 7A0 · [(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-5-[[[4-[6-(ethylamino)-5-(2-piperidin-1-ylethylcarbamoyl) pyridin-2-yl]-2-fluoranyl-phenyl]carbamoylamino]methyl]pyridin-1-ium-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- DPO · Diphosphate · ligand · 2 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 | 812 | 0.80 | 0.83 | 81 | 7A0, DPO |
| 2 | 823 | 0.79 | 0.82 | 83 | DPO, 7A0 |
| 3 | 595 | 0.69 | 0.78 | 49 | empty |
| 4 | 81 | 0.33 | 0.74 | 14 | empty |
| 5 | 55 | 0.31 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4231 Ų buried · 75 hydrogen bonds · protein-protein
Compared structures
- 5LX5 · Crystal structure of visfatin in complex with SAR154782-rp. · the same entry in another collection · chain A against A, TM-score 1.00
- P43490 · AlphaFold monomer V2.0 prediction for nicotinamide phosphoribosyltransferase (P43490) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 5LX5 · PDBe 5LX5 · UniProt P43490
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