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Chlorine in PDB 5s9m: Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%

Enzymatic activity of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%

All present enzymatic activity of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%:
3.1.4.39;

Protein crystallography data

The structure of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%, PDB code: 5s9m was solved by M.Stihle, D.Hunziker, J.Benz, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.37 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.017, 91.009, 119.028, 90, 90, 90
R / Rfree (%) 17.1 / 21.1

Other elements in 5s9m:

The structure of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1% also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Calcium (Ca) 3 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1% (pdb code 5s9m). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%, PDB code: 5s9m:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5s9m

Go back to Chlorine Binding Sites List in 5s9m
Chlorine binding site 1 out of 3 in the Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:30.1
occ:1.00
 CL23 A:YV1901 0.0 30.1 1.0
C21 A:YV1901 1.7 31.9 1.0
C20 A:YV1901 2.7 29.4 1.0
C22 A:YV1901 2.7 29.6 1.0
O A:LEU213 3.5 17.1 1.0
CZ A:PHE274 3.7 51.9 1.0
CH2 A:TRP260 3.7 24.0 1.0
C A:LEU213 3.8 16.8 1.0
CZ3 A:TRP260 3.9 24.5 1.0
C19 A:YV1901 3.9 34.0 1.0
C17 A:YV1901 4.0 33.9 1.0
CB A:ALA217 4.0 19.8 1.0
CD1 A:TYR214 4.1 17.7 1.0
CE2 A:PHE274 4.1 51.1 1.0
CA A:TYR214 4.1 18.9 1.0
N A:TYR214 4.1 16.4 1.0
CB A:LEU213 4.1 18.2 1.0
CE1 A:PHE274 4.5 49.2 1.0
C18 A:YV1901 4.5 32.8 1.0
CA A:LEU213 4.6 18.4 1.0
CB A:TYR214 4.7 19.0 1.0
CG A:TYR214 4.9 18.6 1.0
CE1 A:TYR214 4.9 19.5 1.0
CZ2 A:TRP260 5.0 25.8 1.0

Chlorine binding site 2 out of 3 in 5s9m

Go back to Chlorine Binding Sites List in 5s9m
Chlorine binding site 2 out of 3 in the Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:47.3
occ:1.00
 CL24 A:YV1901 0.0 47.3 1.0
C19 A:YV1901 1.7 34.0 1.0
C20 A:YV1901 2.6 29.4 1.0
C18 A:YV1901 2.8 32.8 1.0
CG2 A:ILE167 3.9 20.9 1.0
C21 A:YV1901 3.9 31.9 1.0
C17 A:YV1901 4.1 33.9 1.0
CB A:SER169 4.2 24.3 1.0
CD2 A:PHE273 4.4 27.4 1.0
CB A:LEU216 4.4 19.6 1.0
OG A:SER169 4.5 28.8 1.0
CD1 A:LEU216 4.5 24.6 1.0
C22 A:YV1901 4.5 29.6 1.0
CE2 A:PHE273 4.6 29.8 1.0
CD2 A:LEU213 4.6 20.4 1.0
CB A:ILE167 4.8 22.7 1.0
O A:LEU213 4.8 17.1 1.0
CD1 A:ILE167 4.8 25.8 1.0
CB A:ALA304 4.9 20.2 1.0

Chlorine binding site 3 out of 3 in 5s9m

Go back to Chlorine Binding Sites List in 5s9m
Chlorine binding site 3 out of 3 in the Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl912

b:46.6
occ:1.00
 ND2 A:ASN801 3.1 21.1 1.0
O A:HOH1017 3.1 37.8 1.0
NH2 A:ARG710 3.2 29.1 1.0
O A:HOH1098 3.3 38.1 1.0
CD A:ARG710 3.6 27.4 1.0
O A:HOH1445 3.6 46.6 1.0
CB A:ALA707 3.8 18.9 1.0
CG A:ASN801 4.0 24.2 1.0
CB A:ASN801 4.0 23.0 1.0
CA A:ALA707 4.1 21.5 1.0
CZ A:ARG710 4.2 29.0 1.0
N A:ASN801 4.3 21.9 1.0
NE A:ARG710 4.3 29.4 1.0
CG A:ARG710 4.7 27.5 1.0
O A:ALA707 4.7 19.3 1.0
CA A:ASN801 4.8 23.0 1.0
C A:ALA707 4.9 21.1 1.0
OG A:SER807 5.0 23.5 1.0

Reference:

D.Hunziker, S.C.Joachim, C.Ullmer, M.G.Rudolph. Crystal Structure of A Rat Autotaxin Complex To Be Published.
Page generated: Sat Jul 12 08:19:09 2025

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