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Chlorine in PDB 5l0k: Crystal Structure of Autotaxin and Compound Pf-8380

Enzymatic activity of Crystal Structure of Autotaxin and Compound Pf-8380

All present enzymatic activity of Crystal Structure of Autotaxin and Compound Pf-8380:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Autotaxin and Compound Pf-8380, PDB code: 5l0k was solved by J.D.Durbin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 96.23 / 2.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.924, 121.422, 156.247, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 27

Other elements in 5l0k:

The structure of Crystal Structure of Autotaxin and Compound Pf-8380 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Autotaxin and Compound Pf-8380 (pdb code 5l0k). 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 Autotaxin and Compound Pf-8380, PDB code: 5l0k:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5l0k

Go back to Chlorine Binding Sites List in 5l0k
Chlorine binding site 1 out of 6 in the Crystal Structure of Autotaxin and Compound Pf-8380


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 Autotaxin and Compound Pf-8380 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl906

b:53.4
occ:1.00
 CL19 A:6ZO906 0.0 53.4 1.0
C5 A:6ZO906 1.7 51.3 1.0
C3 A:6ZO906 2.7 52.3 1.0
C6 A:6ZO906 2.7 52.4 1.0
O A:LEU213 3.4 24.8 1.0
CB A:ALA217 3.5 28.0 1.0
C A:LEU213 3.6 26.1 1.0
CA A:TYR214 3.7 26.4 1.0
N A:TYR214 3.8 25.9 1.0
CZ A:PHE274 3.8 43.1 1.0
CH2 A:TRP260 3.8 30.6 1.0
CD1 A:TYR214 3.9 26.1 1.0
C1 A:6ZO906 4.0 51.9 1.0
CZ3 A:TRP260 4.0 32.4 1.0
C4 A:6ZO906 4.0 52.1 1.0
CB A:LEU213 4.2 26.6 1.0
CE2 A:PHE274 4.2 43.9 1.0
CE1 A:PHE274 4.3 43.9 1.0
CB A:TYR214 4.4 25.6 1.0
CA A:LEU213 4.5 26.5 1.0
C2 A:6ZO906 4.5 51.4 1.0
CG A:TYR214 4.6 24.1 1.0
CE1 A:TYR214 4.8 26.1 1.0
CA A:ALA217 4.8 28.0 1.0
C A:TYR214 4.9 27.6 1.0
N A:ALA217 4.9 28.1 1.0

Chlorine binding site 2 out of 6 in 5l0k

Go back to Chlorine Binding Sites List in 5l0k
Chlorine binding site 2 out of 6 in the Crystal Structure of Autotaxin and Compound Pf-8380


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 Autotaxin and Compound Pf-8380 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl906

b:57.3
occ:1.00
 CL18 A:6ZO906 0.0 57.3 1.0
C4 A:6ZO906 1.7 52.1 1.0
C6 A:6ZO906 2.7 52.4 1.0
C2 A:6ZO906 2.7 51.4 1.0
CG2 A:ILE167 3.9 26.7 1.0
CB A:SER169 4.0 33.3 1.0
C1 A:6ZO906 4.0 51.9 1.0
C5 A:6ZO906 4.0 51.3 1.0
OG A:SER169 4.3 35.6 1.0
CB A:LEU216 4.3 27.8 1.0
CD2 A:LEU213 4.3 26.6 1.0
CD2 A:PHE273 4.3 37.6 1.0
CD1 A:LEU216 4.4 24.2 1.0
C3 A:6ZO906 4.5 52.3 1.0
O A:LEU213 4.7 24.8 1.0
CE2 A:PHE273 4.9 37.6 1.0
CB A:ILE167 5.0 28.2 1.0

Chlorine binding site 3 out of 6 in 5l0k

Go back to Chlorine Binding Sites List in 5l0k
Chlorine binding site 3 out of 6 in the Crystal Structure of Autotaxin and Compound Pf-8380


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 Autotaxin and Compound Pf-8380 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl908

b:34.3
occ:1.00
 N A:ASN230 3.2 32.4 1.0
NH1 A:ARG391 3.5 34.8 1.0
CA A:GLY229 3.7 31.2 1.0
N A:SER231 3.7 33.0 1.0
CD A:LYS208 3.9 36.1 1.0
C A:GLY229 3.9 31.7 1.0
O A:SER231 4.1 35.0 1.0
CA A:ASN230 4.1 32.5 1.0
CE A:LYS208 4.2 36.7 1.0
CG1 A:VAL385 4.2 36.0 1.0
CB A:ASN230 4.2 32.5 1.0
CD1 A:LEU389 4.4 32.8 1.0
C A:ASN230 4.4 32.7 1.0
CD2 A:LEU389 4.5 30.2 1.0
CZ A:ARG391 4.6 36.3 1.0
NZ A:LYS208 4.6 36.3 1.0
CA A:SER231 4.6 34.0 1.0
CB A:SER231 4.7 34.0 1.0
CG A:LYS208 4.7 34.5 1.0
C A:SER231 4.8 34.7 1.0
CG A:LEU389 4.8 30.4 1.0
NH2 A:ARG391 4.9 35.5 1.0
O A:HOH1052 4.9 29.1 1.0

Chlorine binding site 4 out of 6 in 5l0k

Go back to Chlorine Binding Sites List in 5l0k
Chlorine binding site 4 out of 6 in the Crystal Structure of Autotaxin and Compound Pf-8380


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 Autotaxin and Compound Pf-8380 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl907

b:47.8
occ:1.00
 CL19 B:6ZO907 0.0 47.8 1.0
C5 B:6ZO907 1.7 47.6 1.0
C3 B:6ZO907 2.7 48.9 1.0
C6 B:6ZO907 2.7 48.2 1.0
O B:LEU213 3.3 29.9 1.0
C B:LEU213 3.6 29.6 1.0
CB B:ALA217 3.6 31.3 1.0
CZ B:PHE274 3.7 48.8 1.0
CA B:TYR214 3.7 30.9 1.0
N B:TYR214 3.8 30.4 1.0
CD1 B:TYR214 3.9 31.5 1.0
C1 B:6ZO907 4.0 49.8 1.0
CE2 B:PHE274 4.0 47.9 1.0
C4 B:6ZO907 4.0 47.7 1.0
CH2 B:TRP260 4.1 37.1 1.0
CB B:LEU213 4.1 28.7 1.0
CZ3 B:TRP260 4.1 36.8 1.0
CB B:TYR214 4.4 30.7 1.0
CE1 B:PHE274 4.4 48.7 1.0
CA B:LEU213 4.4 29.0 1.0
C2 B:6ZO907 4.5 47.9 1.0
CG B:TYR214 4.6 30.6 1.0
CE1 B:TYR214 4.9 32.1 1.0
CD2 B:PHE274 4.9 48.8 1.0
CA B:ALA217 4.9 31.0 1.0
C B:TYR214 4.9 31.5 1.0
N B:ALA217 5.0 31.3 1.0

Chlorine binding site 5 out of 6 in 5l0k

Go back to Chlorine Binding Sites List in 5l0k
Chlorine binding site 5 out of 6 in the Crystal Structure of Autotaxin and Compound Pf-8380


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 Autotaxin and Compound Pf-8380 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl907

b:48.9
occ:1.00
 CL18 B:6ZO907 0.0 48.9 1.0
C4 B:6ZO907 1.7 47.7 1.0
C6 B:6ZO907 2.7 48.2 1.0
C2 B:6ZO907 2.7 47.9 1.0
CG2 B:ILE167 3.8 33.3 1.0
CB B:SER169 3.8 36.0 1.0
C5 B:6ZO907 4.0 47.6 1.0
C1 B:6ZO907 4.0 49.8 1.0
OG B:SER169 4.1 38.1 1.0
CD2 B:LEU213 4.3 29.2 1.0
CD1 B:LEU216 4.4 29.6 1.0
CD2 B:PHE273 4.4 45.1 1.0
C3 B:6ZO907 4.5 48.9 1.0
CB B:LEU216 4.5 32.3 1.0
O B:LEU213 4.8 29.9 1.0
CB B:ILE167 4.8 32.9 1.0
CE2 B:PHE273 4.9 43.8 1.0

Chlorine binding site 6 out of 6 in 5l0k

Go back to Chlorine Binding Sites List in 5l0k
Chlorine binding site 6 out of 6 in the Crystal Structure of Autotaxin and Compound Pf-8380


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 Autotaxin and Compound Pf-8380 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl909

b:50.6
occ:1.00
 N B:ASN230 3.3 35.7 1.0
NH1 B:ARG391 3.5 33.0 1.0
N B:SER231 3.5 37.4 1.0
CA B:GLY229 3.7 33.8 1.0
O B:SER231 3.9 39.0 1.0
C B:GLY229 3.9 34.7 1.0
CA B:ASN230 4.1 36.7 1.0
CD1 B:LEU389 4.2 37.5 1.0
CG1 B:VAL385 4.2 41.3 1.0
CB B:ASN230 4.3 36.9 1.0
C B:ASN230 4.3 36.8 1.0
CB B:SER231 4.3 37.8 1.0
CA B:SER231 4.3 37.8 1.0
CD2 B:LEU389 4.4 37.3 1.0
NH2 B:ARG391 4.4 35.7 1.0
CZ B:ARG391 4.4 35.0 1.0
CG B:LYS208 4.4 38.9 1.0
CE B:LYS208 4.5 39.6 1.0
C B:SER231 4.6 38.3 1.0
CG B:LEU389 4.7 36.3 1.0
CD B:LYS208 4.9 41.1 1.0
OG B:SER231 4.9 39.1 1.0

Reference:

S.B.Jones, L.A.Pfeifer, T.J.Bleisch, T.J.Beauchamp, J.D.Durbin, V.J.Klimkowski, N.E.Hughes, C.J.Rito, Y.Dao, J.M.Gruber, H.Bui, M.G.Chambers, S.Chandrasekhar, C.Lin, D.J.Mccann, D.R.Mudra, J.L.Oskins, C.A.Swearingen, K.Thirunavukkarasu, B.H.Norman. Novel Autotaxin Inhibitors For the Treatment of Osteoarthritis Pain: Lead Optimization Via Structure-Based Drug Design. Acs Med.Chem.Lett. V. 7 857 2016.
ISSN: ISSN 1948-5875
PubMed: 27660691
DOI: 10.1021/ACSMEDCHEMLETT.6B00207
Page generated: Fri Jul 26 10:58:20 2024

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