MolNFT v1 · #82836 · protein
Crystal structure of sphingosine kinase 1 with inhibitor
3VZC: “Crystal structure of sphingosine kinase 1 with inhibitor”. X-ray diffraction, 1 ligand (UUL), 18 pockets (best druggability 0.80). MolNFT v1 #82836 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VZC
- Type
- protein
- Length
- 2,063 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sphingosine kinase 1
- EC
- 2.7.1.91
- UniProt
- Q9NYA1
- Ligands
- UUL
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 347 | 29% helix, 32% strand | Q9NYA1 |
| B | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 340 | 30% helix, 32% strand | Q9NYA1 |
| C | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 342 | 29% helix, 31% strand | Q9NYA1 |
| D | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 348 | 31% helix, 32% strand | Q9NYA1 |
| E | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 342 | 29% helix, 32% strand | Q9NYA1 |
| F | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 344 | 28% helix, 32% strand | Q9NYA1 |
Ligands and binding sites
- UUL · 4-{[4-(4-chlorophenyl)-1,3-thiazol-2-yl]amino}phenol · ligand · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 2 copies · chains D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.80 | 0.83 | 81 | UUL |
| 2 | 733 | 0.79 | 0.83 | 82 | UUL |
| 3 | 737 | 0.78 | 0.82 | 81 | UUL |
| 4 | 696 | 0.78 | 0.83 | 76 | UUL |
| 5 | 873 | 0.77 | 0.80 | 84 | EDO |
Interfaces
7 interfaces between chains.
- A–E · 888 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 838 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 815 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 807 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 233 Ų buried · 1 hydrogen bond · 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 3VZC · PDBe 3VZC · UniProt Q9NYA1
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