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Chlorine in PDB 3ntg: Crystal Structure of Cox-2 with Selective Compound 23D-(R)

Enzymatic activity of Crystal Structure of Cox-2 with Selective Compound 23D-(R)

All present enzymatic activity of Crystal Structure of Cox-2 with Selective Compound 23D-(R):
1.14.99.1;

Protein crystallography data

The structure of Crystal Structure of Cox-2 with Selective Compound 23D-(R), PDB code: 3ntg was solved by J.L.Wang, D.Limburg, M.J.Graneto, J.C.Carter, J.J.Talley, J.R.Kiefer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.19 / 2.19
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 180.268, 134.273, 122.615, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 25.5

Other elements in 3ntg:

The structure of Crystal Structure of Cox-2 with Selective Compound 23D-(R) also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Iron (Fe) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Cox-2 with Selective Compound 23D-(R) (pdb code 3ntg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Cox-2 with Selective Compound 23D-(R), PDB code: 3ntg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3ntg

Go back to Chlorine Binding Sites List in 3ntg
Chlorine binding site 1 out of 8 in the Crystal Structure of Cox-2 with Selective Compound 23D-(R)


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 Cox-2 with Selective Compound 23D-(R) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:42.5
occ:1.00
 CL8 A:D72701 0.0 42.5 1.0
C4 A:D72701 1.7 42.3 1.0
C5 A:D72701 2.6 42.4 1.0
C1 A:D72701 2.7 42.0 1.0
O9 A:D72701 2.8 41.2 1.0
C19 A:D72701 3.7 45.1 1.0
C17 A:D72701 3.8 43.8 1.0
O A:LEU338 3.9 38.7 1.0
CG A:LEU338 3.9 37.0 1.0
C A:LEU338 3.9 38.3 1.0
C2 A:D72701 3.9 42.1 1.0
CD2 A:PHE504 4.0 37.7 1.0
C3 A:D72701 4.0 42.4 1.0
CE2 A:PHE504 4.0 36.7 1.0
N A:SER339 4.0 38.2 1.0
CB A:LEU338 4.0 37.2 1.0
CG2 A:VAL509 4.0 37.2 1.0
C18 A:D72701 4.0 44.0 1.0
O A:HOH5275 4.1 31.1 1.0
CA A:SER339 4.1 38.8 1.0
C6 A:D72701 4.4 42.0 1.0
CD2 A:LEU338 4.6 36.9 1.0
CA A:LEU338 4.6 37.6 1.0
CG1 A:VAL509 4.8 38.1 1.0
CB A:VAL509 4.8 37.5 1.0
CB A:SER339 4.9 38.8 1.0
CD1 A:LEU338 5.0 37.7 1.0

Chlorine binding site 2 out of 8 in 3ntg

Go back to Chlorine Binding Sites List in 3ntg
Chlorine binding site 2 out of 8 in the Crystal Structure of Cox-2 with Selective Compound 23D-(R)


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 Cox-2 with Selective Compound 23D-(R) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:42.3
occ:1.00
 CL24 A:D72701 0.0 42.3 1.0
C2 A:D72701 1.7 42.1 1.0
C6 A:D72701 2.7 42.0 1.0
C5 A:D72701 2.7 42.4 1.0
O10 A:D72701 2.9 41.4 1.0
C17 A:D72701 2.9 43.8 1.0
O9 A:D72701 3.1 41.2 1.0
OG A:SER516 3.5 33.8 1.0
CG1 A:VAL335 3.5 34.0 1.0
CG2 A:VAL335 3.6 32.7 1.0
CB A:SER516 3.8 32.4 1.0
CA A:ALA513 4.0 34.6 1.0
C4 A:D72701 4.0 42.3 1.0
C3 A:D72701 4.0 42.4 1.0
CG A:LEU517 4.0 33.1 1.0
CB A:VAL335 4.2 34.4 1.0
C13 A:D72701 4.2 41.6 1.0
CD2 A:LEU517 4.2 32.1 1.0
CB A:ALA513 4.3 35.2 1.0
CD1 A:LEU517 4.4 32.6 1.0
O A:ALA513 4.4 34.5 1.0
C18 A:D72701 4.4 44.0 1.0
F23 A:D72701 4.4 42.9 1.0
C1 A:D72701 4.5 42.0 1.0
C14 A:D72701 4.7 42.6 1.0
C A:ALA513 4.7 34.6 1.0
F22 A:D72701 4.8 41.4 1.0
O A:GLY512 4.8 34.0 1.0
N A:ALA513 4.9 34.8 1.0
N A:LEU517 5.0 33.1 1.0
C20 A:D72701 5.0 42.8 1.0

Chlorine binding site 3 out of 8 in 3ntg

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Chlorine binding site 3 out of 8 in the Crystal Structure of Cox-2 with Selective Compound 23D-(R)


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 Cox-2 with Selective Compound 23D-(R) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:41.7
occ:1.00
 CL8 B:D72701 0.0 41.7 1.0
C4 B:D72701 1.7 40.3 1.0
C5 B:D72701 2.7 39.8 1.0
C1 B:D72701 2.7 40.1 1.0
O9 B:D72701 2.9 40.0 1.0
C19 B:D72701 3.6 41.0 1.0
C17 B:D72701 3.7 41.7 1.0
C18 B:D72701 3.8 41.8 1.0
CB B:LEU338 3.9 34.6 1.0
C2 B:D72701 4.0 39.9 1.0
C3 B:D72701 4.0 40.0 1.0
CD2 B:PHE504 4.0 36.3 1.0
CE2 B:PHE504 4.0 34.6 1.0
CG B:LEU338 4.0 34.7 1.0
C B:LEU338 4.0 36.2 1.0
N B:SER339 4.1 35.8 1.0
O B:LEU338 4.1 36.8 1.0
CA B:SER339 4.2 36.0 1.0
CG2 B:VAL509 4.3 38.3 1.0
O B:HOH5264 4.3 35.0 1.0
C6 B:D72701 4.4 39.1 1.0
CA B:LEU338 4.6 35.5 1.0
CG1 B:VAL509 4.6 38.9 1.0
CD2 B:LEU338 4.7 32.2 1.0
CB B:SER339 4.8 35.6 1.0
CB B:VAL509 4.9 38.1 1.0
CA B:VAL509 5.0 37.4 1.0

Chlorine binding site 4 out of 8 in 3ntg

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Chlorine binding site 4 out of 8 in the Crystal Structure of Cox-2 with Selective Compound 23D-(R)


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 Cox-2 with Selective Compound 23D-(R) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:40.1
occ:1.00
 CL24 B:D72701 0.0 40.1 1.0
C2 B:D72701 1.7 39.9 1.0
C6 B:D72701 2.7 39.1 1.0
C5 B:D72701 2.7 39.8 1.0
O10 B:D72701 2.7 40.7 1.0
C17 B:D72701 3.1 41.7 1.0
O9 B:D72701 3.1 40.0 1.0
CG2 B:VAL335 3.5 32.5 1.0
CG1 B:VAL335 3.6 33.8 1.0
OG B:SER516 3.7 35.8 1.0
CB B:SER516 3.9 35.7 1.0
CA B:ALA513 4.0 36.3 1.0
C3 B:D72701 4.0 40.0 1.0
C4 B:D72701 4.0 40.3 1.0
C13 B:D72701 4.1 40.3 1.0
CG B:LEU517 4.1 39.5 1.0
CB B:VAL335 4.2 34.1 1.0
CB B:ALA513 4.3 37.2 1.0
O B:ALA513 4.4 36.3 1.0
F23 B:D72701 4.4 38.9 1.0
CD1 B:LEU517 4.4 39.5 1.0
F22 B:D72701 4.5 41.5 1.0
C1 B:D72701 4.5 40.1 1.0
C18 B:D72701 4.6 41.8 1.0
CD2 B:LEU517 4.6 39.1 1.0
C14 B:D72701 4.6 39.9 1.0
C B:ALA513 4.7 36.7 1.0
N B:ALA513 4.8 35.9 1.0
O B:GLY512 4.9 34.4 1.0
N B:LEU517 4.9 37.3 1.0

Chlorine binding site 5 out of 8 in 3ntg

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Chlorine binding site 5 out of 8 in the Crystal Structure of Cox-2 with Selective Compound 23D-(R)


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 Cox-2 with Selective Compound 23D-(R) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl701

b:48.0
occ:1.00
 CL8 C:D72701 0.0 48.0 1.0
C4 C:D72701 1.7 45.3 1.0
C1 C:D72701 2.7 45.1 1.0
C5 C:D72701 2.7 44.6 1.0
O9 C:D72701 2.9 44.3 1.0
C19 C:D72701 3.8 44.6 1.0
C17 C:D72701 3.8 44.1 1.0
C18 C:D72701 3.9 43.7 1.0
C3 C:D72701 3.9 45.2 1.0
C2 C:D72701 4.0 44.6 1.0
N C:SER339 4.0 43.4 1.0
CA C:SER339 4.0 43.8 1.0
C C:LEU338 4.0 44.1 1.0
CD2 C:PHE504 4.1 42.5 1.0
O C:LEU338 4.1 45.1 1.0
CG C:LEU338 4.2 43.2 1.0
CB C:LEU338 4.2 43.1 1.0
CE2 C:PHE504 4.2 42.0 1.0
CG2 C:VAL509 4.2 42.7 1.0
C6 C:D72701 4.4 44.6 1.0
CD2 C:LEU338 4.4 40.6 1.0
CG1 C:VAL509 4.7 42.7 1.0
CA C:LEU338 4.8 43.9 1.0
CB C:SER339 4.8 43.7 1.0
CB C:VAL509 4.9 42.7 1.0
CA C:VAL509 5.0 41.7 1.0

Chlorine binding site 6 out of 8 in 3ntg

Go back to Chlorine Binding Sites List in 3ntg
Chlorine binding site 6 out of 8 in the Crystal Structure of Cox-2 with Selective Compound 23D-(R)


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 Cox-2 with Selective Compound 23D-(R) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl701

b:47.4
occ:1.00
 CL24 C:D72701 0.0 47.4 1.0
C2 C:D72701 1.7 44.6 1.0
C6 C:D72701 2.7 44.6 1.0
C5 C:D72701 2.7 44.6 1.0
O10 C:D72701 2.8 45.5 1.0
C17 C:D72701 3.0 44.1 1.0
O9 C:D72701 3.1 44.3 1.0
CG1 C:VAL335 3.5 41.5 1.0
CG2 C:VAL335 3.5 40.0 1.0
OG C:SER516 3.8 40.8 1.0
CA C:ALA513 3.9 40.7 1.0
C3 C:D72701 4.0 45.2 1.0
C4 C:D72701 4.0 45.3 1.0
CB C:SER516 4.1 40.8 1.0
CG C:LEU517 4.1 42.8 1.0
CB C:VAL335 4.1 40.5 1.0
C13 C:D72701 4.2 44.7 1.0
CB C:ALA513 4.3 41.5 1.0
O C:ALA513 4.4 40.4 1.0
CD2 C:LEU517 4.4 41.6 1.0
F22 C:D72701 4.4 43.2 1.0
F23 C:D72701 4.4 45.1 1.0
C18 C:D72701 4.5 43.7 1.0
C1 C:D72701 4.5 45.1 1.0
CD1 C:LEU517 4.6 42.0 1.0
C14 C:D72701 4.6 44.2 1.0
C C:ALA513 4.7 40.8 1.0
N C:ALA513 4.8 40.0 1.0
C19 C:D72701 4.9 44.6 1.0
O C:GLY512 4.9 38.4 1.0
N C:LEU517 5.0 41.7 1.0

Chlorine binding site 7 out of 8 in 3ntg

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Chlorine binding site 7 out of 8 in the Crystal Structure of Cox-2 with Selective Compound 23D-(R)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Cox-2 with Selective Compound 23D-(R) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl701

b:47.3
occ:1.00
 CL8 D:D72701 0.0 47.3 1.0
C4 D:D72701 1.7 45.2 1.0
C1 D:D72701 2.7 43.7 1.0
C5 D:D72701 2.7 43.8 1.0
O9 D:D72701 2.9 45.4 1.0
C19 D:D72701 3.7 48.1 1.0
O D:LEU338 3.8 40.5 1.0
C17 D:D72701 3.9 46.2 1.0
C D:LEU338 3.9 40.5 1.0
C3 D:D72701 3.9 42.6 1.0
C2 D:D72701 4.0 43.5 1.0
CG2 D:VAL509 4.0 41.7 1.0
CA D:SER339 4.0 41.5 1.0
N D:SER339 4.0 40.7 1.0
CB D:LEU338 4.1 39.3 1.0
CD2 D:PHE504 4.1 39.7 1.0
CG D:LEU338 4.1 40.2 1.0
CE2 D:PHE504 4.1 39.4 1.0
C18 D:D72701 4.3 46.0 1.0
C6 D:D72701 4.4 41.6 1.0
CB D:SER339 4.7 41.1 1.0
CA D:LEU338 4.7 39.9 1.0
CD2 D:LEU338 4.7 39.6 1.0
CG1 D:VAL509 4.7 41.2 1.0
CB D:VAL509 4.8 41.3 1.0

Chlorine binding site 8 out of 8 in 3ntg

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Chlorine binding site 8 out of 8 in the Crystal Structure of Cox-2 with Selective Compound 23D-(R)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Cox-2 with Selective Compound 23D-(R) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl701

b:41.2
occ:1.00
 CL24 D:D72701 0.0 41.2 1.0
C2 D:D72701 1.7 43.5 1.0
C6 D:D72701 2.7 41.6 1.0
C5 D:D72701 2.7 43.8 1.0
O10 D:D72701 2.8 41.8 1.0
C17 D:D72701 3.0 46.2 1.0
O9 D:D72701 3.0 45.4 1.0
CG1 D:VAL335 3.6 37.6 1.0
OG D:SER516 3.7 39.9 1.0
CG2 D:VAL335 3.7 36.6 1.0
CA D:ALA513 3.8 40.9 1.0
CB D:SER516 3.8 39.5 1.0
CG D:LEU517 4.0 41.7 1.0
C3 D:D72701 4.0 42.6 1.0
C4 D:D72701 4.0 45.2 1.0
CB D:ALA513 4.1 41.4 1.0
CD2 D:LEU517 4.1 42.7 1.0
C13 D:D72701 4.2 41.9 1.0
O D:ALA513 4.2 40.0 1.0
CB D:VAL335 4.3 37.1 1.0
F23 D:D72701 4.4 42.1 1.0
CD1 D:LEU517 4.4 41.7 1.0
C18 D:D72701 4.4 46.0 1.0
C D:ALA513 4.5 40.6 1.0
C1 D:D72701 4.5 43.7 1.0
C14 D:D72701 4.6 42.2 1.0
F22 D:D72701 4.7 42.2 1.0
N D:ALA513 4.7 40.7 1.0
O D:GLY512 4.8 39.7 1.0
N D:LEU517 4.9 40.3 1.0
C20 D:D72701 5.0 44.9 1.0

Reference:

J.L.Wang, D.Limburg, M.J.Graneto, J.Springer, J.R.Hamper, S.Liao, J.L.Pawlitz, R.G.Kurumbail, T.Maziasz, J.J.Talley, J.R.Kiefer, J.Carter. The Novel Benzopyran Class of Selective Cyclooxygenase-2 Inhibitors. Part 2: the Second Clinical Candidate Having A Shorter and Favorable Human Half-Life. Bioorg.Med.Chem.Lett. V. 20 7159 2010.
ISSN: ISSN 0960-894X
PubMed: 20709553
DOI: 10.1016/J.BMCL.2010.07.054
Page generated: Sun Jul 21 01:13:39 2024

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