Research workbench
Sphingosine kinase 1 in complex with pf-543
Analyse Sphingosine kinase 1 in complex with pf-543 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V24
- Type
- protein
- Length
- 700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sphingosine kinase 1
- EC
- 2.7.1.91
- UniProt
- Q9NYA1
- Ligands
- GYR
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 351 | 32% helix, 31% strand | Q9NYA1 |
| B | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 349 | 31% helix, 32% strand | Q9NYA1 |
Ligands and binding sites
- GYR · {(2R)-1-[4-({3-methyl-5-[(phenylsulfonyl)methyl]phenoxy}methyl)benzyl]pyrrolidin-2-yl}methanol · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.86 | 0.87 | 111 | GYR |
| 2 | 497 | 0.82 | 0.88 | 60 | GYR |
| 3 | 106 | 0.47 | 0.79 | 14 | empty |
| 4 | 51 | 0.29 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 623 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 Q9NYA1
- Elsewhere: RCSB PDB 4V24 · PDBe 4V24 · UniProt Q9NYA1
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