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Chlorine in PDB 4otj: The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide

Enzymatic activity of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide

All present enzymatic activity of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide:
1.14.99.1;

Protein crystallography data

The structure of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide, PDB code: 4otj was solved by S.Xu, M.J.Uddin, S.Banerjee, L.J.Marnett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.11 / 2.11
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 180.712, 133.943, 122.223, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 19.9

Other elements in 4otj:

The structure of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide (pdb code 4otj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide, PDB code: 4otj:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4otj

Go back to Chlorine Binding Sites List in 4otj
Chlorine binding site 1 out of 4 in the The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl706

b:45.1
occ:1.00
 CL A:IXP706 0.0 45.1 1.0
CBT A:IXP706 1.7 37.5 1.0
CBS A:IXP706 2.7 37.8 1.0
CBU A:IXP706 2.7 37.3 1.0
CZ2 A:TRP387 3.4 23.5 1.0
CA A:GLY526 3.9 30.2 1.0
SD A:MET522 3.9 32.8 1.0
CBR A:IXP706 4.0 38.3 1.0
CBV A:IXP706 4.0 37.9 1.0
O A:MET522 4.2 29.8 1.0
CE2 A:TRP387 4.2 23.1 1.0
NE1 A:TRP387 4.3 22.6 1.0
CG A:MET522 4.3 26.4 1.0
CH2 A:TRP387 4.3 24.5 1.0
CD2 A:TYR385 4.3 26.4 1.0
CE2 A:TYR385 4.4 27.3 1.0
CE1 A:PHE381 4.4 32.3 1.0
CBQ A:IXP706 4.5 38.8 1.0
O A:LEU384 4.5 31.5 1.0
CB A:LEU384 4.5 35.0 1.0
CG A:TYR385 4.6 24.4 1.0
C A:GLY526 4.6 32.5 1.0
C A:LEU384 4.7 30.8 1.0
CZ A:TYR385 4.7 27.7 1.0
N A:GLY526 4.8 31.2 1.0
CD1 A:TYR385 4.9 23.1 1.0
O A:GLY526 4.9 36.3 1.0
CD1 A:PHE381 4.9 29.4 1.0
CA A:TYR385 4.9 22.4 1.0
N A:TYR385 4.9 25.5 1.0
CE1 A:TYR385 5.0 23.4 1.0

Chlorine binding site 2 out of 4 in 4otj

Go back to Chlorine Binding Sites List in 4otj
Chlorine binding site 2 out of 4 in the The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl707

b:48.4
occ:1.00
 CL B:IXP707 0.0 48.4 1.0
CBT B:IXP707 1.7 38.9 1.0
CBS B:IXP707 2.7 38.8 1.0
CBU B:IXP707 2.7 38.5 1.0
CZ2 B:TRP387 3.2 32.3 1.0
SD B:MET522 3.7 33.2 1.0
CA B:GLY526 3.9 30.6 1.0
CE2 B:TRP387 4.0 31.1 1.0
CBR B:IXP707 4.0 40.3 1.0
CBV B:IXP707 4.0 39.0 1.0
CG B:MET522 4.1 32.8 1.0
NE1 B:TRP387 4.1 30.6 1.0
CH2 B:TRP387 4.2 30.8 1.0
O B:MET522 4.2 27.8 1.0
CD2 B:TYR385 4.3 29.0 1.0
CB B:LEU384 4.3 37.0 1.0
CE2 B:TYR385 4.4 29.9 1.0
O B:LEU384 4.5 31.3 1.0
CBQ B:IXP707 4.5 40.3 1.0
CG B:TYR385 4.6 27.9 1.0
CE1 B:PHE381 4.6 28.3 1.0
C B:LEU384 4.7 32.1 1.0
C B:GLY526 4.7 31.0 1.0
CZ B:TYR385 4.8 30.2 1.0
CG B:LEU384 4.8 45.9 1.0
CA B:TYR385 4.9 25.8 1.0
N B:GLY526 4.9 31.8 1.0
N B:TYR385 4.9 27.4 1.0
CD1 B:TYR385 4.9 26.4 1.0

Chlorine binding site 3 out of 4 in 4otj

Go back to Chlorine Binding Sites List in 4otj
Chlorine binding site 3 out of 4 in the The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl706

b:44.2
occ:1.00
 CL C:IXP706 0.0 44.2 1.0
CBT C:IXP706 1.6 34.6 1.0
CBU C:IXP706 2.6 34.1 1.0
CBS C:IXP706 2.6 33.3 1.0
CD1 C:LEU384 2.8 54.5 1.0
CZ2 C:TRP387 3.4 20.4 1.0
SD C:MET522 3.8 29.3 1.0
CA C:GLY526 3.8 22.7 1.0
CBR C:IXP706 3.9 35.1 1.0
CBV C:IXP706 3.9 34.7 1.0
O C:MET522 4.1 22.7 1.0
CG C:MET522 4.2 26.0 1.0
CG C:LEU384 4.2 46.3 1.0
CE2 C:TRP387 4.2 24.8 1.0
NE1 C:TRP387 4.3 23.9 1.0
CH2 C:TRP387 4.3 20.2 1.0
CD2 C:TYR385 4.4 26.6 1.0
CE1 C:PHE381 4.4 25.5 1.0
CBQ C:IXP706 4.4 36.5 1.0
O C:LEU384 4.4 27.1 1.0
CE2 C:TYR385 4.5 25.2 1.0
C C:GLY526 4.6 23.7 1.0
CG C:TYR385 4.6 26.0 1.0
CB C:LEU384 4.6 32.8 1.0
C C:LEU384 4.7 25.8 1.0
N C:GLY526 4.7 25.6 1.0
CD2 C:LEU384 4.7 50.1 1.0
CD1 C:PHE381 4.9 24.7 1.0
CZ C:TYR385 4.9 26.5 1.0
CA C:TYR385 4.9 23.4 1.0
N C:TYR385 4.9 21.9 1.0
C C:MET522 5.0 24.3 1.0
CD1 C:TYR385 5.0 24.7 1.0
O C:GLY526 5.0 29.0 1.0

Chlorine binding site 4 out of 4 in 4otj

Go back to Chlorine Binding Sites List in 4otj
Chlorine binding site 4 out of 4 in the The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl707

b:44.8
occ:1.00
 CL D:IXP707 0.0 44.8 1.0
CBT D:IXP707 1.7 35.5 1.0
CBS D:IXP707 2.7 35.3 1.0
CBU D:IXP707 2.7 35.9 1.0
CZ2 D:TRP387 3.3 23.7 1.0
SD D:MET522 3.6 29.5 1.0
CG D:MET522 3.9 27.2 1.0
CA D:GLY526 3.9 22.2 1.0
O D:MET522 4.0 24.3 1.0
CBV D:IXP707 4.0 36.6 1.0
CBR D:IXP707 4.0 36.5 1.0
CE2 D:TRP387 4.1 25.8 1.0
CH2 D:TRP387 4.2 25.0 1.0
NE1 D:TRP387 4.2 26.0 1.0
CBQ D:IXP707 4.5 37.2 1.0
CB D:LEU384 4.6 32.5 1.0
O D:LEU384 4.6 29.0 1.0
C D:GLY526 4.7 27.4 1.0
CD2 D:TYR385 4.7 30.2 1.0
C D:MET522 4.7 27.1 1.0
CE2 D:TYR385 4.7 29.4 1.0
CE1 D:PHE381 4.8 23.9 1.0
N D:GLY526 4.9 24.7 1.0
C D:LEU384 4.9 28.8 1.0
CE2 D:PHE518 4.9 27.7 1.0
CG D:TYR385 5.0 26.3 1.0

Reference:

M.J.Uddin, B.C.Crews, S.Xu, K.Ghebreselasie, S.Banerjee, C.K.Daniel, P.J.Kingsley, L.J.Marnett. Antitumor Activity of Cytotoxic Cyclooxygenase-2 Inhibitors To Be Published.
Page generated: Fri Jul 11 20:09:00 2025

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