Research workbench
Crystal structure of sphingosine kinase 1 with inhibitor and ADP
Analyse Crystal structure of sphingosine kinase 1 with inhibitor and ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VZD
- Type
- protein
- Length
- 2,076 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, ADP, POP, MG, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 349 | 32% helix, 33% strand | Q9NYA1 |
| B | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 342 | 32% helix, 32% strand | Q9NYA1 |
| C, F | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 346 | 29% helix, 32% strand | Q9NYA1 |
| E | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 344 | 31% helix, 32% strand | Q9NYA1 |
Ligands and binding sites
- UUL · 4-{[4-(4-chlorophenyl)-1,3-thiazol-2-yl]amino}phenol · ligand · 7 copies · chains A, B, C, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, E
- POP · Pyrophosphate 2- · ligand · chains B
- MG · Magnesium ion · metal · 3 copies · chains B, C, E
- CL · Chloride ion · ion · 3 copies · chains B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.81 | 0.90 | 54 | UUL, POP, MG |
| 2 | 556 | 0.81 | 0.87 | 72 | UUL |
| 3 | 477 | 0.80 | 0.87 | 71 | UUL, ADP, MG |
| 4 | 530 | 0.80 | 0.86 | 67 | UUL |
| 5 | 454 | 0.79 | 0.87 | 66 | UUL |
Interfaces
7 interfaces between chains.
- B–C · 848 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 833 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 830 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 794 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 240 Ų buried · 4 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 3VZD · PDBe 3VZD · UniProt Q9NYA1
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