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Chlorine in PDB 4q6r: 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

Enzymatic activity of 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

All present enzymatic activity of 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:
4.1.2.27;

Protein crystallography data

The structure of 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, PDB code: 4q6r was solved by H.Srinivas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.66 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.985, 130.532, 68.224, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the 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 (pdb code 4q6r). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the 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, PDB code: 4q6r:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4q6r

Go back to Chlorine Binding Sites List in 4q6r
Chlorine binding site 1 out of 2 in the 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


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 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl903

b:70.4
occ:1.00
 CL1 A:30J903 0.0 70.4 1.0
C2 A:30J903 1.7 67.6 1.0
C13 A:30J903 2.6 67.1 1.0
C3 A:30J903 2.7 64.2 1.0
C11 A:30J903 3.9 65.4 1.0
C5 A:30J903 4.0 63.7 1.0
CZ B:PHE545 4.0 67.8 1.0
CG A:ASP176 4.0 77.0 1.0
CB A:ASP176 4.0 62.5 1.0
CE1 B:PHE545 4.1 69.0 1.0
OD1 A:ASP176 4.1 77.5 1.0
CG A:PRO175 4.1 62.5 1.0
CD A:PRO175 4.4 58.0 1.0
C10 A:30J903 4.4 64.6 1.0
OD2 A:ASP176 4.4 84.5 1.0
N A:ASP176 4.5 60.1 1.0
C30 A:30J903 4.9 60.8 1.0
CA A:ASP176 4.9 60.2 1.0

Chlorine binding site 2 out of 2 in 4q6r

Go back to Chlorine Binding Sites List in 4q6r
Chlorine binding site 2 out of 2 in the 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


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 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:49.7
occ:1.00
 CL1 B:30J602 0.0 49.7 1.0
C2 B:30J602 1.7 43.3 1.0
C13 B:30J602 2.6 40.6 1.0
C3 B:30J602 2.7 41.3 1.0
CG B:ASP176 3.8 44.9 1.0
C11 B:30J602 3.9 39.5 1.0
C5 B:30J602 3.9 41.4 1.0
OD1 B:ASP176 3.9 42.2 1.0
CB B:ASP176 4.0 39.4 1.0
CZ A:PHE545 4.1 40.7 1.0
OD2 B:ASP176 4.1 52.0 1.0
CE1 A:PHE545 4.3 42.8 1.0
C10 B:30J602 4.4 39.7 1.0
CG B:PRO175 4.5 42.4 1.0
CD B:PRO175 4.6 38.0 1.0
N B:ASP176 4.6 38.6 1.0
O B:HOH832 4.8 47.4 1.0
CA B:ASP176 5.0 37.7 1.0

Reference:

S.Weiler, N.Braendlin, C.Beerli, C.Bergsdorf, A.Schubart, H.Srinivas, B.Oberhauser, A.Billich. Orally Active 7-Substituted (4-Benzylphthalazin-1-Yl)-2-Methylpiperazin-1- Yl]Nicotinonitriles As Active-Site Inhibitors of Sphingosine 1-Phosphate Lyase For the Treatment of Multiple Sclerosis. J.Med.Chem. V. 57 5074 2014.
ISSN: ISSN 0022-2623
PubMed: 24809814
DOI: 10.1021/JM500338N
Page generated: Fri Jul 11 20:42:26 2025

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