Iron 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:
Iron Binding Sites:
The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the
Structure of Compound 5C-S Bound at the Active Site of Cox-2, PDB code: 3ln0:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3ln0
Go back to
Iron Binding Sites List in 3ln0
Iron binding site 1 out
of 4 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 Iron with other atoms in the Fe 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:Fe605
b:24.5
occ:1.00
|
FE
|
A:HEM605
|
0.0
|
24.5
|
1.0
|
NC
|
A:HEM605
|
2.0
|
25.0
|
1.0
|
NA
|
A:HEM605
|
2.0
|
27.5
|
1.0
|
ND
|
A:HEM605
|
2.1
|
24.9
|
1.0
|
NE2
|
A:HIS374
|
2.1
|
24.6
|
1.0
|
NB
|
A:HEM605
|
2.1
|
25.5
|
1.0
|
O
|
A:HOH4121
|
2.3
|
27.1
|
1.0
|
CD2
|
A:HIS374
|
3.0
|
24.3
|
1.0
|
C4C
|
A:HEM605
|
3.0
|
24.9
|
1.0
|
C1A
|
A:HEM605
|
3.0
|
28.2
|
1.0
|
C1D
|
A:HEM605
|
3.0
|
24.8
|
1.0
|
C1C
|
A:HEM605
|
3.0
|
25.3
|
1.0
|
C4A
|
A:HEM605
|
3.0
|
28.3
|
1.0
|
C4D
|
A:HEM605
|
3.1
|
24.3
|
1.0
|
CE1
|
A:HIS374
|
3.1
|
24.9
|
1.0
|
C1B
|
A:HEM605
|
3.1
|
26.0
|
1.0
|
C4B
|
A:HEM605
|
3.2
|
26.1
|
1.0
|
CHD
|
A:HEM605
|
3.4
|
24.6
|
1.0
|
CHA
|
A:HEM605
|
3.4
|
26.0
|
1.0
|
CHB
|
A:HEM605
|
3.5
|
26.2
|
1.0
|
CHC
|
A:HEM605
|
3.5
|
25.8
|
1.0
|
CG
|
A:HIS374
|
4.1
|
23.7
|
1.0
|
ND1
|
A:HIS374
|
4.2
|
24.3
|
1.0
|
C3C
|
A:HEM605
|
4.2
|
23.9
|
1.0
|
C2A
|
A:HEM605
|
4.2
|
31.1
|
1.0
|
C2C
|
A:HEM605
|
4.2
|
24.3
|
1.0
|
C3A
|
A:HEM605
|
4.2
|
29.2
|
1.0
|
NE2
|
A:GLN189
|
4.3
|
20.3
|
1.0
|
C3D
|
A:HEM605
|
4.3
|
24.0
|
1.0
|
C2D
|
A:HEM605
|
4.3
|
24.5
|
1.0
|
C2B
|
A:HEM605
|
4.4
|
26.5
|
1.0
|
C3B
|
A:HEM605
|
4.4
|
26.5
|
1.0
|
NE2
|
A:HIS193
|
4.4
|
23.2
|
1.0
|
CE1
|
A:HIS193
|
4.8
|
23.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 3ln0
Go back to
Iron Binding Sites List in 3ln0
Iron binding site 2 out
of 4 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 Iron with other atoms in the Fe 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
|
B:Fe605
b:26.5
occ:1.00
|
FE
|
B:HEM605
|
0.0
|
26.5
|
1.0
|
NC
|
B:HEM605
|
2.0
|
26.7
|
1.0
|
ND
|
B:HEM605
|
2.0
|
26.4
|
1.0
|
NA
|
B:HEM605
|
2.1
|
28.5
|
1.0
|
NB
|
B:HEM605
|
2.1
|
27.8
|
1.0
|
NE2
|
B:HIS374
|
2.2
|
24.8
|
1.0
|
C4C
|
B:HEM605
|
3.0
|
25.8
|
1.0
|
C1D
|
B:HEM605
|
3.0
|
25.0
|
1.0
|
C1C
|
B:HEM605
|
3.0
|
26.3
|
1.0
|
C4D
|
B:HEM605
|
3.0
|
25.5
|
1.0
|
CD2
|
B:HIS374
|
3.1
|
24.2
|
1.0
|
C1A
|
B:HEM605
|
3.1
|
29.6
|
1.0
|
C4A
|
B:HEM605
|
3.1
|
29.0
|
1.0
|
C4B
|
B:HEM605
|
3.1
|
27.1
|
1.0
|
C1B
|
B:HEM605
|
3.1
|
28.4
|
1.0
|
CE1
|
B:HIS374
|
3.2
|
24.9
|
1.0
|
CHD
|
B:HEM605
|
3.3
|
25.6
|
1.0
|
CHC
|
B:HEM605
|
3.4
|
26.8
|
1.0
|
CHA
|
B:HEM605
|
3.4
|
28.0
|
1.0
|
CHB
|
B:HEM605
|
3.5
|
28.8
|
1.0
|
C2C
|
B:HEM605
|
4.2
|
25.9
|
1.0
|
C3C
|
B:HEM605
|
4.2
|
25.5
|
1.0
|
CG
|
B:HIS374
|
4.2
|
23.8
|
1.0
|
C2D
|
B:HEM605
|
4.2
|
24.8
|
1.0
|
ND1
|
B:HIS374
|
4.2
|
24.2
|
1.0
|
C3D
|
B:HEM605
|
4.2
|
24.9
|
1.0
|
NE2
|
B:GLN189
|
4.3
|
20.4
|
1.0
|
C2A
|
B:HEM605
|
4.3
|
30.9
|
1.0
|
C3A
|
B:HEM605
|
4.3
|
29.8
|
1.0
|
C2B
|
B:HEM605
|
4.3
|
29.3
|
1.0
|
NE2
|
B:HIS193
|
4.3
|
23.5
|
1.0
|
C3B
|
B:HEM605
|
4.3
|
29.4
|
1.0
|
O
|
B:HOH4515
|
4.5
|
32.0
|
1.0
|
CE1
|
B:HIS193
|
4.7
|
23.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 3ln0
Go back to
Iron Binding Sites List in 3ln0
Iron binding site 3 out
of 4 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 Iron with other atoms in the Fe 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
|
C:Fe605
b:25.8
occ:1.00
|
FE
|
C:HEM605
|
0.0
|
25.8
|
1.0
|
NC
|
C:HEM605
|
2.0
|
25.6
|
1.0
|
NA
|
C:HEM605
|
2.0
|
26.9
|
1.0
|
ND
|
C:HEM605
|
2.0
|
25.2
|
1.0
|
O
|
C:HOH4116
|
2.1
|
30.1
|
1.0
|
NB
|
C:HEM605
|
2.1
|
25.8
|
1.0
|
NE2
|
C:HIS374
|
2.2
|
24.8
|
1.0
|
C4C
|
C:HEM605
|
3.0
|
26.1
|
1.0
|
C1C
|
C:HEM605
|
3.0
|
25.3
|
1.0
|
C4D
|
C:HEM605
|
3.0
|
24.8
|
1.0
|
C1D
|
C:HEM605
|
3.0
|
24.2
|
1.0
|
C1A
|
C:HEM605
|
3.0
|
28.7
|
1.0
|
C4A
|
C:HEM605
|
3.1
|
27.5
|
1.0
|
CD2
|
C:HIS374
|
3.1
|
24.1
|
1.0
|
C4B
|
C:HEM605
|
3.1
|
26.9
|
1.0
|
C1B
|
C:HEM605
|
3.1
|
27.2
|
1.0
|
CE1
|
C:HIS374
|
3.2
|
24.8
|
1.0
|
CHD
|
C:HEM605
|
3.4
|
24.0
|
1.0
|
CHA
|
C:HEM605
|
3.4
|
26.0
|
1.0
|
CHC
|
C:HEM605
|
3.4
|
27.1
|
1.0
|
CHB
|
C:HEM605
|
3.5
|
26.8
|
1.0
|
O
|
C:HOH4219
|
4.0
|
40.6
|
1.0
|
C3C
|
C:HEM605
|
4.2
|
24.5
|
1.0
|
C2C
|
C:HEM605
|
4.2
|
25.2
|
1.0
|
C3D
|
C:HEM605
|
4.3
|
22.3
|
1.0
|
CG
|
C:HIS374
|
4.3
|
23.7
|
1.0
|
NE2
|
C:GLN189
|
4.3
|
20.4
|
1.0
|
C2D
|
C:HEM605
|
4.3
|
22.6
|
1.0
|
ND1
|
C:HIS374
|
4.3
|
24.4
|
1.0
|
C2A
|
C:HEM605
|
4.3
|
29.9
|
1.0
|
C3A
|
C:HEM605
|
4.3
|
27.9
|
1.0
|
NE2
|
C:HIS193
|
4.3
|
23.5
|
1.0
|
C3B
|
C:HEM605
|
4.3
|
28.7
|
1.0
|
C2B
|
C:HEM605
|
4.3
|
29.3
|
1.0
|
CE1
|
C:HIS193
|
4.7
|
23.6
|
1.0
|
|
Iron binding site 4 out
of 4 in 3ln0
Go back to
Iron Binding Sites List in 3ln0
Iron binding site 4 out
of 4 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 Iron with other atoms in the Fe 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
|
D:Fe605
b:22.3
occ:1.00
|
FE
|
D:HEM605
|
0.0
|
22.3
|
1.0
|
NC
|
D:HEM605
|
2.0
|
24.1
|
1.0
|
NA
|
D:HEM605
|
2.0
|
25.6
|
1.0
|
ND
|
D:HEM605
|
2.1
|
23.3
|
1.0
|
NE2
|
D:HIS374
|
2.1
|
24.7
|
1.0
|
NB
|
D:HEM605
|
2.1
|
24.1
|
1.0
|
O
|
D:HOH4018
|
2.4
|
23.3
|
1.0
|
CD2
|
D:HIS374
|
3.0
|
24.1
|
1.0
|
C1C
|
D:HEM605
|
3.0
|
25.2
|
1.0
|
C4C
|
D:HEM605
|
3.0
|
23.1
|
1.0
|
C1A
|
D:HEM605
|
3.0
|
26.6
|
1.0
|
C4D
|
D:HEM605
|
3.0
|
23.9
|
1.0
|
C1D
|
D:HEM605
|
3.1
|
22.6
|
1.0
|
C4A
|
D:HEM605
|
3.1
|
25.5
|
1.0
|
CE1
|
D:HIS374
|
3.1
|
24.7
|
1.0
|
C4B
|
D:HEM605
|
3.1
|
24.6
|
1.0
|
C1B
|
D:HEM605
|
3.2
|
24.9
|
1.0
|
CHD
|
D:HEM605
|
3.4
|
22.1
|
1.0
|
CHA
|
D:HEM605
|
3.4
|
26.0
|
1.0
|
CHC
|
D:HEM605
|
3.4
|
24.8
|
1.0
|
CHB
|
D:HEM605
|
3.6
|
24.6
|
1.0
|
CG
|
D:HIS374
|
4.1
|
23.5
|
1.0
|
ND1
|
D:HIS374
|
4.2
|
24.2
|
1.0
|
C2C
|
D:HEM605
|
4.2
|
24.9
|
1.0
|
C3C
|
D:HEM605
|
4.2
|
24.9
|
1.0
|
NE2
|
D:GLN189
|
4.2
|
20.4
|
1.0
|
C2A
|
D:HEM605
|
4.3
|
28.7
|
1.0
|
C3D
|
D:HEM605
|
4.3
|
23.8
|
1.0
|
C2D
|
D:HEM605
|
4.3
|
21.4
|
1.0
|
C3A
|
D:HEM605
|
4.3
|
26.2
|
1.0
|
C3B
|
D:HEM605
|
4.4
|
25.6
|
1.0
|
C2B
|
D:HEM605
|
4.4
|
25.4
|
1.0
|
NE2
|
D:HIS193
|
4.4
|
23.2
|
1.0
|
O
|
D:HOH4557
|
4.4
|
35.1
|
1.0
|
CE1
|
D:HIS193
|
4.7
|
23.6
|
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 Aug 4 14:31:29 2024
|