Chlorine in PDB 3ln0: Structure of Compound 5C-S Bound at the Active Site of Cox-2
Enzymatic activity of Structure of Compound 5C-S Bound at the Active Site of Cox-2
All present enzymatic activity of Structure of Compound 5C-S Bound at the Active Site of Cox-2:
1.14.99.1;
Protein crystallography data
The structure of Structure of Compound 5C-S Bound at the Active Site of Cox-2, PDB code: 3ln0
was solved by
J.R.Kiefer,
R.G.Kurumbail,
W.C.Stallings,
J.L.Pawlitz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.96 /
2.20
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
181.015,
135.201,
124.291,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.9 /
23.8
|
Other elements in 3ln0:
The structure of Structure of Compound 5C-S Bound at the Active Site of Cox-2 also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Structure of Compound 5C-S Bound at the Active Site of Cox-2
(pdb code 3ln0). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the
Structure of Compound 5C-S Bound at the Active Site of Cox-2, PDB code: 3ln0:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Chlorine binding site 1 out
of 8 in 3ln0
Go back to
Chlorine Binding Sites List in 3ln0
Chlorine binding site 1 out
of 8 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl701
b:35.0
occ:1.00
|
CL1
|
A:52B701
|
0.0
|
35.0
|
1.0
|
C4
|
A:52B701
|
1.7
|
29.4
|
1.0
|
C5
|
A:52B701
|
2.6
|
28.9
|
1.0
|
C1
|
A:52B701
|
2.7
|
27.9
|
1.0
|
NH1
|
A:ARG106
|
3.8
|
47.4
|
1.0
|
CD1
|
A:LEU517
|
3.8
|
29.4
|
1.0
|
C2
|
A:52B701
|
3.9
|
28.8
|
1.0
|
C3
|
A:52B701
|
4.0
|
27.5
|
1.0
|
CB
|
A:ALA513
|
4.0
|
23.8
|
1.0
|
OH
|
A:TYR341
|
4.1
|
33.4
|
1.0
|
CZ
|
A:ARG106
|
4.4
|
45.4
|
1.0
|
CE2
|
A:TYR341
|
4.4
|
31.4
|
1.0
|
C6
|
A:52B701
|
4.4
|
27.9
|
1.0
|
CG
|
A:LEU517
|
4.5
|
28.3
|
1.0
|
CD
|
A:ARG106
|
4.6
|
44.4
|
1.0
|
CG2
|
A:VAL102
|
4.7
|
38.1
|
1.0
|
CD2
|
A:LEU517
|
4.7
|
29.8
|
1.0
|
CG1
|
A:VAL335
|
4.7
|
24.5
|
1.0
|
CZ
|
A:TYR341
|
4.8
|
32.0
|
1.0
|
NE
|
A:ARG106
|
4.8
|
44.7
|
1.0
|
CA
|
A:ALA513
|
4.9
|
24.2
|
1.0
|
|
Chlorine binding site 2 out
of 8 in 3ln0
Go back to
Chlorine Binding Sites List in 3ln0
Chlorine binding site 2 out
of 8 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl701
b:34.4
occ:1.00
|
CL2
|
A:52B701
|
0.0
|
34.4
|
1.0
|
C2
|
A:52B701
|
1.7
|
28.8
|
1.0
|
C5
|
A:52B701
|
2.7
|
28.9
|
1.0
|
C6
|
A:52B701
|
2.7
|
27.9
|
1.0
|
O11
|
A:52B701
|
2.8
|
26.0
|
1.0
|
CA
|
A:SER339
|
3.5
|
27.5
|
1.0
|
CG1
|
A:VAL509
|
3.6
|
25.2
|
1.0
|
CB
|
A:SER339
|
3.9
|
27.4
|
1.0
|
N
|
A:SER339
|
3.9
|
27.1
|
1.0
|
C4
|
A:52B701
|
3.9
|
29.4
|
1.0
|
C3
|
A:52B701
|
4.0
|
27.5
|
1.0
|
CG2
|
A:VAL509
|
4.0
|
25.3
|
1.0
|
C9
|
A:52B701
|
4.1
|
26.9
|
1.0
|
C
|
A:LEU338
|
4.2
|
27.1
|
1.0
|
O
|
A:LEU338
|
4.2
|
27.0
|
1.0
|
CB
|
A:VAL509
|
4.4
|
25.6
|
1.0
|
C1
|
A:52B701
|
4.5
|
27.9
|
1.0
|
F2
|
A:52B701
|
4.5
|
25.8
|
1.0
|
F1
|
A:52B701
|
4.5
|
27.0
|
1.0
|
OH
|
A:TYR341
|
4.5
|
33.4
|
1.0
|
C14
|
A:52B701
|
4.6
|
26.4
|
1.0
|
C
|
A:SER339
|
4.7
|
28.0
|
1.0
|
CB
|
A:LEU338
|
4.7
|
27.2
|
1.0
|
O
|
A:SER339
|
4.9
|
28.1
|
1.0
|
CZ
|
A:TYR341
|
4.9
|
32.0
|
1.0
|
O
|
A:HOH5156
|
5.0
|
32.1
|
1.0
|
|
Chlorine binding site 3 out
of 8 in 3ln0
Go back to
Chlorine Binding Sites List in 3ln0
Chlorine binding site 3 out
of 8 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl701
b:34.4
occ:1.00
|
CL1
|
B:52B701
|
0.0
|
34.4
|
1.0
|
C4
|
B:52B701
|
1.7
|
29.6
|
1.0
|
C5
|
B:52B701
|
2.6
|
29.6
|
1.0
|
C1
|
B:52B701
|
2.7
|
28.1
|
1.0
|
NH1
|
B:ARG106
|
3.7
|
47.4
|
1.0
|
CD1
|
B:LEU517
|
3.8
|
29.6
|
1.0
|
C2
|
B:52B701
|
3.9
|
29.8
|
1.0
|
CB
|
B:ALA513
|
3.9
|
23.9
|
1.0
|
C3
|
B:52B701
|
4.0
|
28.1
|
1.0
|
OH
|
B:TYR341
|
4.1
|
33.1
|
1.0
|
CZ
|
B:ARG106
|
4.3
|
45.4
|
1.0
|
CE2
|
B:TYR341
|
4.5
|
31.4
|
1.0
|
C6
|
B:52B701
|
4.5
|
28.2
|
1.0
|
CD
|
B:ARG106
|
4.5
|
44.3
|
1.0
|
CG
|
B:LEU517
|
4.5
|
28.3
|
1.0
|
CG2
|
B:VAL102
|
4.6
|
38.1
|
1.0
|
NE
|
B:ARG106
|
4.7
|
44.8
|
1.0
|
CD2
|
B:LEU517
|
4.7
|
29.7
|
1.0
|
CZ
|
B:TYR341
|
4.8
|
31.9
|
1.0
|
CG1
|
B:VAL335
|
4.8
|
24.6
|
1.0
|
CA
|
B:ALA513
|
4.9
|
24.2
|
1.0
|
CG
|
B:ARG106
|
5.0
|
43.8
|
1.0
|
|
Chlorine binding site 4 out
of 8 in 3ln0
Go back to
Chlorine Binding Sites List in 3ln0
Chlorine binding site 4 out
of 8 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl701
b:32.1
occ:1.00
|
CL2
|
B:52B701
|
0.0
|
32.1
|
1.0
|
C2
|
B:52B701
|
1.7
|
29.8
|
1.0
|
C6
|
B:52B701
|
2.7
|
28.2
|
1.0
|
C5
|
B:52B701
|
2.7
|
29.6
|
1.0
|
O11
|
B:52B701
|
2.8
|
28.1
|
1.0
|
CG1
|
B:VAL509
|
3.5
|
25.1
|
1.0
|
CA
|
B:SER339
|
3.6
|
27.6
|
1.0
|
CG2
|
B:VAL509
|
3.9
|
25.2
|
1.0
|
C4
|
B:52B701
|
3.9
|
29.6
|
1.0
|
C3
|
B:52B701
|
3.9
|
28.1
|
1.0
|
CB
|
B:SER339
|
4.0
|
27.4
|
1.0
|
N
|
B:SER339
|
4.0
|
27.2
|
1.0
|
C9
|
B:52B701
|
4.1
|
27.1
|
1.0
|
CB
|
B:VAL509
|
4.3
|
25.8
|
1.0
|
C
|
B:LEU338
|
4.3
|
27.1
|
1.0
|
O
|
B:LEU338
|
4.3
|
26.8
|
1.0
|
F2
|
B:52B701
|
4.4
|
28.0
|
1.0
|
C1
|
B:52B701
|
4.4
|
28.1
|
1.0
|
OH
|
B:TYR341
|
4.5
|
33.1
|
1.0
|
F1
|
B:52B701
|
4.5
|
27.5
|
1.0
|
C14
|
B:52B701
|
4.6
|
27.7
|
1.0
|
C
|
B:SER339
|
4.8
|
27.8
|
1.0
|
CB
|
B:LEU338
|
4.8
|
27.2
|
1.0
|
O
|
B:SER339
|
4.9
|
28.0
|
1.0
|
CZ
|
B:TYR341
|
4.9
|
31.9
|
1.0
|
|
Chlorine binding site 5 out
of 8 in 3ln0
Go back to
Chlorine Binding Sites List in 3ln0
Chlorine binding site 5 out
of 8 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl701
b:33.0
occ:1.00
|
CL1
|
C:52B701
|
0.0
|
33.0
|
1.0
|
C4
|
C:52B701
|
1.7
|
28.1
|
1.0
|
C5
|
C:52B701
|
2.7
|
27.6
|
1.0
|
C1
|
C:52B701
|
2.7
|
26.7
|
1.0
|
CD1
|
C:LEU517
|
3.8
|
29.6
|
1.0
|
NH1
|
C:ARG106
|
3.8
|
47.4
|
1.0
|
C2
|
C:52B701
|
3.9
|
27.6
|
1.0
|
CB
|
C:ALA513
|
4.0
|
23.8
|
1.0
|
C3
|
C:52B701
|
4.0
|
25.8
|
1.0
|
OH
|
C:TYR341
|
4.2
|
33.2
|
1.0
|
CG
|
C:LEU517
|
4.4
|
28.4
|
1.0
|
C6
|
C:52B701
|
4.5
|
26.1
|
1.0
|
CZ
|
C:ARG106
|
4.5
|
45.4
|
1.0
|
CE2
|
C:TYR341
|
4.5
|
31.4
|
1.0
|
CD2
|
C:LEU517
|
4.6
|
29.8
|
1.0
|
CD
|
C:ARG106
|
4.7
|
44.3
|
1.0
|
CG2
|
C:VAL102
|
4.7
|
38.2
|
1.0
|
CG1
|
C:VAL335
|
4.7
|
24.5
|
1.0
|
NE
|
C:ARG106
|
4.8
|
44.8
|
1.0
|
CZ
|
C:TYR341
|
4.9
|
31.8
|
1.0
|
CA
|
C:ALA513
|
4.9
|
24.1
|
1.0
|
|
Chlorine binding site 6 out
of 8 in 3ln0
Go back to
Chlorine Binding Sites List in 3ln0
Chlorine binding site 6 out
of 8 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl701
b:31.4
occ:1.00
|
CL2
|
C:52B701
|
0.0
|
31.4
|
1.0
|
C2
|
C:52B701
|
1.7
|
27.6
|
1.0
|
C5
|
C:52B701
|
2.7
|
27.6
|
1.0
|
C6
|
C:52B701
|
2.7
|
26.1
|
1.0
|
O11
|
C:52B701
|
2.8
|
25.7
|
1.0
|
CG1
|
C:VAL509
|
3.5
|
25.2
|
1.0
|
CA
|
C:SER339
|
3.6
|
27.5
|
1.0
|
C4
|
C:52B701
|
3.9
|
28.1
|
1.0
|
CG2
|
C:VAL509
|
3.9
|
25.1
|
1.0
|
C3
|
C:52B701
|
3.9
|
25.8
|
1.0
|
CB
|
C:SER339
|
4.0
|
27.3
|
1.0
|
N
|
C:SER339
|
4.0
|
27.2
|
1.0
|
C9
|
C:52B701
|
4.2
|
24.9
|
1.0
|
C
|
C:LEU338
|
4.3
|
27.2
|
1.0
|
O
|
C:LEU338
|
4.3
|
26.9
|
1.0
|
CB
|
C:VAL509
|
4.3
|
25.7
|
1.0
|
F2
|
C:52B701
|
4.4
|
25.1
|
1.0
|
C1
|
C:52B701
|
4.4
|
26.7
|
1.0
|
F1
|
C:52B701
|
4.5
|
26.7
|
1.0
|
OH
|
C:TYR341
|
4.6
|
33.2
|
1.0
|
C14
|
C:52B701
|
4.6
|
25.7
|
1.0
|
C
|
C:SER339
|
4.8
|
27.8
|
1.0
|
CB
|
C:LEU338
|
4.8
|
27.3
|
1.0
|
O
|
C:SER339
|
4.9
|
27.8
|
1.0
|
CZ
|
C:TYR341
|
5.0
|
31.8
|
1.0
|
|
Chlorine binding site 7 out
of 8 in 3ln0
Go back to
Chlorine Binding Sites List in 3ln0
Chlorine binding site 7 out
of 8 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl701
b:34.6
occ:1.00
|
CL1
|
D:52B701
|
0.0
|
34.6
|
1.0
|
C4
|
D:52B701
|
1.7
|
30.6
|
1.0
|
C5
|
D:52B701
|
2.6
|
30.6
|
1.0
|
C1
|
D:52B701
|
2.7
|
28.6
|
1.0
|
NH1
|
D:ARG106
|
3.8
|
47.3
|
1.0
|
CD1
|
D:LEU517
|
3.8
|
29.5
|
1.0
|
C2
|
D:52B701
|
3.9
|
30.5
|
1.0
|
C3
|
D:52B701
|
4.0
|
28.7
|
1.0
|
CB
|
D:ALA513
|
4.0
|
23.9
|
1.0
|
OH
|
D:TYR341
|
4.1
|
33.2
|
1.0
|
CE2
|
D:TYR341
|
4.4
|
31.5
|
1.0
|
CZ
|
D:ARG106
|
4.4
|
45.5
|
1.0
|
C6
|
D:52B701
|
4.5
|
29.3
|
1.0
|
CG
|
D:LEU517
|
4.6
|
28.3
|
1.0
|
CD
|
D:ARG106
|
4.7
|
44.4
|
1.0
|
CG2
|
D:VAL102
|
4.7
|
38.1
|
1.0
|
CG1
|
D:VAL335
|
4.7
|
24.5
|
1.0
|
CZ
|
D:TYR341
|
4.7
|
31.8
|
1.0
|
CD2
|
D:LEU517
|
4.8
|
29.8
|
1.0
|
NE
|
D:ARG106
|
4.8
|
44.8
|
1.0
|
CA
|
D:ALA513
|
5.0
|
24.2
|
1.0
|
|
Chlorine binding site 8 out
of 8 in 3ln0
Go back to
Chlorine Binding Sites List in 3ln0
Chlorine binding site 8 out
of 8 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl701
b:35.3
occ:1.00
|
CL2
|
D:52B701
|
0.0
|
35.3
|
1.0
|
C2
|
D:52B701
|
1.7
|
30.5
|
1.0
|
C6
|
D:52B701
|
2.7
|
29.3
|
1.0
|
C5
|
D:52B701
|
2.7
|
30.6
|
1.0
|
O11
|
D:52B701
|
2.8
|
27.4
|
1.0
|
CA
|
D:SER339
|
3.5
|
27.5
|
1.0
|
CG1
|
D:VAL509
|
3.6
|
25.3
|
1.0
|
CB
|
D:SER339
|
3.9
|
27.4
|
1.0
|
N
|
D:SER339
|
3.9
|
27.2
|
1.0
|
C4
|
D:52B701
|
3.9
|
30.6
|
1.0
|
C3
|
D:52B701
|
4.0
|
28.7
|
1.0
|
CG2
|
D:VAL509
|
4.0
|
25.2
|
1.0
|
C9
|
D:52B701
|
4.1
|
26.3
|
1.0
|
O
|
D:LEU338
|
4.2
|
26.9
|
1.0
|
C
|
D:LEU338
|
4.2
|
27.2
|
1.0
|
F1
|
D:52B701
|
4.4
|
26.9
|
1.0
|
CB
|
D:VAL509
|
4.4
|
25.4
|
1.0
|
C1
|
D:52B701
|
4.4
|
28.6
|
1.0
|
F2
|
D:52B701
|
4.5
|
22.9
|
1.0
|
OH
|
D:TYR341
|
4.6
|
33.2
|
1.0
|
C14
|
D:52B701
|
4.6
|
25.4
|
1.0
|
C
|
D:SER339
|
4.7
|
27.9
|
1.0
|
CB
|
D:LEU338
|
4.7
|
27.3
|
1.0
|
O
|
D:SER339
|
4.8
|
28.1
|
1.0
|
CZ
|
D:TYR341
|
4.9
|
31.8
|
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: Sat Jul 20 23:32:15 2024
|