Research workbench
Crystal structure of human sphingosine-1-phosphate lyase in complex with inhibitor 6-[(2R)-4-(4-benzyl-7-chlorophthalazin-1-yl)-2- methylpiperazin-1-YL]PYRIDINE-3-carbonitrile
Analyse Crystal structure of human sphingosine-1-phosphate lyase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q6R
- Type
- protein
- Length
- 887 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sphingosine-1-phosphate lyase 1
- EC
- 4.1.2.27
- UniProt
- O95470
- Ligands
- 30J, PO4
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sphingosine-1-phosphate lyase 1 (EC 4.1.2.27) | protein | 443 | 44% helix, 14% strand | O95470 |
| B | Sphingosine-1-phosphate lyase 1 (EC 4.1.2.27) | protein | 444 | 43% helix, 14% strand | O95470 |
Ligands and binding sites
- 30J · 6-[(2R)-4-(4-benzyl-7-chlorophthalazin-1-yl)-2-methylpiperazin-1-yl]pyridine-3-carbonitrile · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
- SIN · Succinic acid · additive · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.79 | 0.85 | 58 | 30J, PO4 |
| 2 | 116 | 0.77 | 0.97 | 35 | empty |
| 3 | 525 | 0.77 | 0.84 | 56 | SIN, 30J |
| 4 | 84 | 0.49 | 0.82 | 16 | empty |
| 5 | 59 | 0.45 | 0.83 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 6825 Ų buried · 86 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 4Q6R · Crystal structure of human sphingosine-1-phosphate lyase in complex with inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- O95470 · AlphaFold monomer V2.0 prediction for sphingosine-1-phosphate lyase 1 (O95470) · a predicted model of the same protein · 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 O95470
- Elsewhere: RCSB PDB 4Q6R · PDBe 4Q6R · UniProt O95470
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