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Chlorine in PDB 2x5o: Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase

Enzymatic activity of Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase

All present enzymatic activity of Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase:
6.3.2.9;

Protein crystallography data

The structure of Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase, PDB code: 2x5o was solved by N.Zidar, T.Tomasic, R.Sink, V.Rupnik, A.Kovac, S.Turk, C.Contreras-Martel, A.Dessen, D.Blanot, S.Gobec, A.Zega, L.Peterlin-Masic, D.Kikelja, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.36 / 1.46
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 66.091, 66.091, 135.781, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase (pdb code 2x5o). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase, PDB code: 2x5o:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2x5o

Go back to Chlorine Binding Sites List in 2x5o
Chlorine binding site 1 out of 4 in the Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1453

b:36.3
occ:1.00
 ND1 A:HIS309 3.1 25.6 1.0
N A:ASN310 3.3 23.1 1.0
CA A:HIS309 3.6 23.0 1.0
CE1 A:HIS309 3.8 30.2 1.0
CG A:HIS309 3.9 27.7 1.0
C A:HIS309 3.9 21.7 1.0
CB A:HIS309 4.3 25.9 1.0
O A:HOH2408 4.3 11.0 1.0
CA A:ASN310 4.3 24.4 1.0
OD1 A:ASN310 4.4 29.4 1.0
O A:GLU308 4.4 21.8 1.0
NE2 A:HIS309 4.7 29.5 1.0
N A:HIS309 4.7 21.3 1.0
CD2 A:HIS309 4.8 25.7 1.0
C A:GLU308 5.0 20.7 1.0

Chlorine binding site 2 out of 4 in 2x5o

Go back to Chlorine Binding Sites List in 2x5o
Chlorine binding site 2 out of 4 in the Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1458

b:36.1
occ:1.00
 O A:HOH2080 3.4 25.1 1.0
O A:HOH2038 3.4 27.6 1.0
N A:MET38 3.8 32.0 1.0
CA A:ARG37 4.0 21.9 1.0
CB A:ARG37 4.3 24.4 1.0
C A:ARG37 4.4 24.6 1.0
CG A:ARG37 4.7 21.2 1.0
CB A:MET38 4.7 36.3 0.5
CB A:MET38 4.8 35.4 0.5
CA A:MET38 4.9 33.0 0.5
CA A:MET38 4.9 32.7 0.5
O A:HOH2074 4.9 33.5 1.0

Chlorine binding site 3 out of 4 in 2x5o

Go back to Chlorine Binding Sites List in 2x5o
Chlorine binding site 3 out of 4 in the Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1459

b:25.6
occ:1.00
 OE2 A:GLU253 2.7 27.2 1.0
O A:LYS254 2.9 16.6 1.0
O A:HOH2381 3.5 16.2 1.0
CD A:GLU253 3.6 33.5 1.0
O A:HOH2382 3.8 21.8 1.0
CG1 A:VAL255 3.8 16.3 1.0
CG A:GLU253 3.8 22.0 1.0
C A:LYS254 3.9 14.8 1.0
CA A:VAL255 3.9 16.0 1.0
CB A:VAL255 4.3 16.8 1.0
N A:VAL255 4.4 15.1 1.0
OE1 A:GLU253 4.8 35.8 1.0
C A:VAL255 5.0 16.3 1.0

Chlorine binding site 4 out of 4 in 2x5o

Go back to Chlorine Binding Sites List in 2x5o
Chlorine binding site 4 out of 4 in the Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors of Murd Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1505

b:50.0
occ:1.00
 O A:HOH2446 3.1 17.7 1.0
ND2 A:ASN363 3.6 35.3 1.0
O A:HOH2445 3.9 22.0 1.0
CB A:ASN363 4.5 24.6 1.0
CG A:ASN363 4.5 28.7 1.0
O A:HOH2443 4.6 23.8 1.0
CA A:GLY361 4.8 35.0 1.0
O A:ASN360 4.8 31.6 1.0
O A:HOH2447 4.9 24.2 1.0

Reference:

N.Zidar, T.Tomasic, R.Sink, V.Rupnik, A.Kovac, S.Turk, D.Patin, D.Blanot, C.Contreras Martel, A.Dessen, M.Muller Premru, A.Zega, S.Gobec, L.Peterlin Masic, D.Kikelj. Discovery of Novel 5-Benzylidenerhodanine and 5-Benzylidenethiazolidine-2,4-Dione Inhibitors of Murd Ligase. J. Med. Chem. V. 53 6584 2010.
ISSN: ISSN 1520-4804
PubMed: 20804196
DOI: 10.1021/JM100285G
Page generated: Fri Jul 11 01:46:21 2025

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