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Crystal structure of SPHK1 with inhibitor

Analyse Crystal structure of SPHK1 with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4L02
Type: protein
Length: 1,045 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sphingosine kinase 1
EC: 2.7.1.91
UniProt: Q9NYA1
Ligands: 1V2
Pockets: 9 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sphingosine kinase 1 (EC 2.7.1.91)	protein	360	33% helix, 31% strand	Q9NYA1
B	Sphingosine kinase 1 (EC 2.7.1.91)	protein	340	31% helix, 34% strand	Q9NYA1
C	Sphingosine kinase 1 (EC 2.7.1.91)	protein	345	31% helix, 32% strand	Q9NYA1

Ligands and binding sites

1V2 · (2R,4S)-1-[2-(4-{[4-(3,4-dichlorophenyl)-1,3-thiazol-2-yl]amino}phenyl)ethyl]-2-(hydroxymethyl)piperidin-4-ol · ligand · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	923	0.84	0.86	91	1V2
2	649	0.84	0.88	79	1V2
3	476	0.82	0.89	77	1V2
4	324	0.69	0.82	26	empty
5	93	0.63	0.89	19	empty

Interfaces

3 interfaces between chains.

A–C · 590 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 584 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 307 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4L02 · Crystal Structure of SphK1 with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
Q9NYA1 · AlphaFold monomer V2.0 prediction for sphingosine kinase 1 (Q9NYA1) · a predicted model of the same protein · chain B 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 Q9NYA1
Elsewhere: RCSB PDB 4L02 · PDBe 4L02 · UniProt Q9NYA1

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