Chlorine in PDB 4l02: Crystal Structure of SPHK1 with Inhibitor

All present enzymatic activity of Crystal Structure of SPHK1 with Inhibitor:
2.7.1.91;

The structure of Crystal Structure of SPHK1 with Inhibitor, PDB code: 4l02 was solved by X.Min, N.Walker, Z.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	102.575, 225.684, 106.411, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.5

The binding sites of Chlorine atom in the Crystal Structure of SPHK1 with Inhibitor (pdb code 4l02). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of SPHK1 with Inhibitor, PDB code: 4l02:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of SPHK1 with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of SPHK1 with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:54.2 occ:1.00 CL1 A:1V2401 0.0 54.2 1.0 C14 A:1V2401 1.7 48.4 1.0 C15 A:1V2401 2.7 49.0 1.0 C13 A:1V2401 2.7 45.1 1.0 CL2 A:1V2401 3.1 53.8 1.0 CD2 A:LEU261 3.4 22.4 1.0 CD1 A:LEU268 3.7 26.0 1.0 C12 A:1V2401 4.0 42.3 1.0 C16 A:1V2401 4.0 46.8 1.0 CD1 A:ILE174 4.2 28.6 1.0 CB A:ALA274 4.2 25.0 1.0 SD A:MET306 4.3 25.5 0.7 CD2 A:PHE288 4.5 26.7 1.0 CG A:PHE288 4.5 26.9 1.0 C17 A:1V2401 4.5 44.7 1.0 CG A:LEU261 4.6 22.6 1.0 CG A:LEU268 4.7 26.4 1.0 CB A:PHE288 4.7 26.8 1.0 CB A:LEU261 4.7 22.8 1.0 CD1 A:PHE288 4.9 27.2 1.0 CE2 A:PHE288 4.9 27.0 1.0 CD1 A:LEU259 4.9 26.9 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of SPHK1 with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of SPHK1 with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:53.8 occ:1.00 CL2 A:1V2401 0.0 53.8 1.0 C15 A:1V2401 1.7 49.0 1.0 C14 A:1V2401 2.7 48.4 1.0 C16 A:1V2401 2.7 46.8 1.0 CL1 A:1V2401 3.1 54.2 1.0 CD1 A:PHE288 3.3 27.2 1.0 CD2 A:HIS311 3.5 36.7 1.0 NE2 A:HIS311 3.6 36.4 1.0 CE1 A:PHE288 3.7 27.1 1.0 CD1 A:LEU319 3.8 28.4 1.0 CG A:PHE288 3.8 26.9 1.0 C13 A:1V2401 4.0 45.1 1.0 C17 A:1V2401 4.0 44.7 1.0 CB A:PHE288 4.3 26.8 1.0 CD2 A:LEU319 4.4 29.0 1.0 CZ A:PHE288 4.5 27.3 1.0 C12 A:1V2401 4.5 42.3 1.0 CD2 A:PHE288 4.6 26.7 1.0 CG A:LEU319 4.7 28.7 1.0 CG A:HIS311 4.8 37.2 1.0 O A:ALA274 4.8 26.0 1.0 CE2 A:PHE288 4.9 27.0 1.0 CE1 A:HIS311 4.9 36.7 1.0 SD A:MET312 4.9 36.7 0.7

Chlorine binding site 3 out of 6 in the Crystal Structure of SPHK1 with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of SPHK1 with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:67.4 occ:1.00 CL1 B:1V2401 0.0 67.4 1.0 C14 B:1V2401 1.7 66.3 1.0 C15 B:1V2401 2.7 68.3 1.0 C13 B:1V2401 2.7 64.2 1.0 CL2 B:1V2401 3.0 75.5 1.0 CD2 B:LEU261 3.5 36.0 1.0 C16 B:1V2401 4.0 67.0 1.0 C12 B:1V2401 4.0 62.2 1.0 CB B:ALA274 4.1 33.6 1.0 CD2 B:LEU268 4.2 30.7 1.0 CG B:PHE288 4.4 38.2 1.0 SD B:MET306 4.4 38.4 0.7 CD1 B:ILE174 4.4 44.1 1.0 CB B:PHE288 4.5 38.3 1.0 C17 B:1V2401 4.5 64.6 1.0 CD2 B:PHE288 4.5 38.2 1.0 CE B:MET306 4.7 38.2 1.0 CD1 B:PHE288 4.7 38.4 1.0 CG B:LEU261 4.8 36.1 1.0 CB B:LEU261 4.9 36.1 1.0 O B:ALA274 4.9 33.5 1.0 CA B:ALA274 4.9 33.6 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of SPHK1 with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of SPHK1 with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:75.5 occ:1.00 CL2 B:1V2401 0.0 75.5 1.0 C15 B:1V2401 1.7 68.3 1.0 C14 B:1V2401 2.7 66.3 1.0 C16 B:1V2401 2.7 67.0 1.0 CL1 B:1V2401 3.0 67.4 1.0 CD1 B:PHE288 3.4 38.4 1.0 CD2 B:HIS311 3.5 37.1 1.0 CD1 B:LEU319 3.6 42.1 1.0 NE2 B:HIS311 3.7 36.9 1.0 CE1 B:PHE288 3.9 38.5 1.0 CG B:PHE288 3.9 38.2 1.0 C13 B:1V2401 4.0 64.2 1.0 C17 B:1V2401 4.0 64.6 1.0 CD2 B:LEU319 4.1 42.1 1.0 CB B:PHE288 4.2 38.3 1.0 CG B:LEU319 4.5 41.8 1.0 C12 B:1V2401 4.5 62.2 1.0 O B:ALA274 4.7 33.5 1.0 CG B:HIS311 4.7 37.2 1.0 CZ B:PHE288 4.8 38.7 1.0 CD2 B:PHE288 4.8 38.2 1.0 CE1 B:HIS311 4.9 36.8 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of SPHK1 with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of SPHK1 with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl401 b:65.3 occ:1.00 CL1 C:1V2401 0.0 65.3 1.0 C14 C:1V2401 1.7 63.8 1.0 C15 C:1V2401 2.7 65.3 1.0 C13 C:1V2401 2.7 60.2 1.0 CL2 C:1V2401 3.1 72.7 1.0 CD2 C:LEU261 3.5 31.0 1.0 CD2 C:LEU268 4.0 30.8 1.0 C16 C:1V2401 4.0 62.9 1.0 C12 C:1V2401 4.0 57.2 1.0 SD C:MET306 4.1 41.6 0.7 CG C:PHE288 4.2 39.7 1.0 CB C:ALA274 4.2 35.2 1.0 CD2 C:PHE288 4.2 40.2 1.0 CD1 C:ILE174 4.4 30.6 1.0 CB C:PHE288 4.4 38.6 1.0 C17 C:1V2401 4.5 60.0 1.0 CD1 C:PHE288 4.5 40.0 1.0 CE2 C:PHE288 4.7 40.9 1.0 CG C:LEU261 4.7 30.7 1.0 CB C:LEU261 4.8 30.9 1.0 CE1 C:PHE288 4.9 40.7 1.0 CD1 C:LEU259 5.0 33.5 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of SPHK1 with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of SPHK1 with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl401 b:72.7 occ:1.00 CL2 C:1V2401 0.0 72.7 1.0 C15 C:1V2401 1.7 65.3 1.0 C14 C:1V2401 2.7 63.8 1.0 C16 C:1V2401 2.7 62.9 1.0 CL1 C:1V2401 3.1 65.3 1.0 CD1 C:PHE288 3.3 40.0 1.0 CD2 C:HIS311 3.4 51.1 1.0 CE1 C:PHE288 3.6 40.7 1.0 NE2 C:HIS311 3.6 51.3 1.0 CD1 C:LEU319 3.6 43.5 1.0 CD2 C:LEU319 3.9 43.6 1.0 CG C:PHE288 4.0 39.7 1.0 C13 C:1V2401 4.0 60.2 1.0 C17 C:1V2401 4.0 60.0 1.0 CZ C:PHE288 4.4 40.7 1.0 CG C:LEU319 4.4 43.5 1.0 CB C:PHE288 4.5 38.6 1.0 C12 C:1V2401 4.5 57.2 1.0 CG C:HIS311 4.6 50.9 1.0 O C:ALA274 4.6 37.0 1.0 CD2 C:PHE288 4.7 40.2 1.0 SD C:MET312 4.8 47.2 0.7 CE1 C:HIS311 4.8 51.2 1.0 CE2 C:PHE288 4.9 40.9 1.0

D.J.Gustin, Y.Li, M.L.Brown, X.Min, M.J.Schmitt, M.Wanska, X.Wang, R.Connors, S.Johnstone, M.Cardozo, A.C.Cheng, S.Jeffries, B.Franks, S.Li, S.Shen, M.Wong, H.Wesche, G.Xu, T.J.Carlson, M.Plant, K.Morgenstern, K.Rex, J.Schmitt, A.Coxon, N.Walker, F.Kayser, Z.Wang. Structure Guided Design of A Series of Sphingosine Kinase (Sphk) Inhibitors. Bioorg.Med.Chem.Lett. V. 23 4608 2013.
ISSN: ISSN 0960-894X
PubMed: 23845219
DOI: 10.1016/J.BMCL.2013.06.030