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Chlorine in PDB 5i7a: Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid]

Enzymatic activity of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid]

All present enzymatic activity of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid]:
2.5.1.113;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid], PDB code: 5i7a was solved by R.Schnell, S.Maric, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.80 / 2.08
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.479, 76.044, 81.627, 94.66, 108.75, 107.29
R / Rfree (%) 17 / 20.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid] (pdb code 5i7a). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid], PDB code: 5i7a:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5i7a

Go back to Chlorine Binding Sites List in 5i7a
Chlorine binding site 1 out of 8 in the Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:39.8
occ:1.00
 CL1 A:68Q401 0.0 39.8 1.0
CAT A:68Q401 1.7 31.2 1.0
CAS A:68Q401 2.6 32.1 1.0
CAK A:68Q401 2.7 29.4 1.0
CL2 A:68Q401 3.0 35.9 1.0
CA A:SER265 3.9 24.8 1.0
CAJ A:68Q401 3.9 29.7 1.0
CAR A:68Q401 3.9 27.8 1.0
CB A:ALA268 4.1 24.3 1.0
CB A:SER265 4.3 25.9 1.0
N A:SER265 4.3 25.8 1.0
CAI A:68Q401 4.4 29.1 1.0
O A:ILE264 4.6 25.8 1.0
CB A:PRO210 4.6 35.0 1.0
C A:ILE264 4.6 26.1 1.0
CG2 A:ILE264 4.7 30.2 1.0
CG A:PRO210 4.9 35.4 1.0
C A:SER265 4.9 24.0 1.0
NAN A:68Q401 5.0 25.2 1.0

Chlorine binding site 2 out of 8 in 5i7a

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Chlorine binding site 2 out of 8 in the Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:35.9
occ:1.00
 CL2 A:68Q401 0.0 35.9 1.0
CAS A:68Q401 1.7 32.1 1.0
CAT A:68Q401 2.7 31.2 1.0
CAJ A:68Q401 2.7 29.7 1.0
CL1 A:68Q401 3.0 39.8 1.0
CB A:ALA268 3.3 24.3 1.0
C A:GLU209 3.4 30.7 1.0
N A:PRO210 3.4 32.3 1.0
CA A:GLU209 3.6 30.2 1.0
O A:ALA208 3.7 26.9 1.0
CD A:PRO210 3.8 34.5 1.0
C A:ALA208 3.8 26.4 1.0
N A:GLU209 3.8 28.1 1.0
O A:GLU209 3.8 29.4 1.0
CAK A:68Q401 4.0 29.4 1.0
CAI A:68Q401 4.0 29.1 1.0
CA A:PRO210 4.1 35.4 1.0
CB A:ALA208 4.3 26.2 1.0
CB A:PRO210 4.5 35.0 1.0
CG A:PRO210 4.5 35.4 1.0
CAR A:68Q401 4.5 27.8 1.0
CA A:ALA208 4.7 24.8 1.0
CA A:ALA268 4.7 23.8 1.0
CB A:VAL242 5.0 30.9 1.0

Chlorine binding site 3 out of 8 in 5i7a

Go back to Chlorine Binding Sites List in 5i7a
Chlorine binding site 3 out of 8 in the Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:41.9
occ:1.00
 CL1 B:68Q401 0.0 41.9 1.0
CAT B:68Q401 1.7 32.2 1.0
CAS B:68Q401 2.7 31.4 1.0
CAK B:68Q401 2.7 31.4 1.0
CL2 B:68Q401 3.1 35.9 1.0
CA B:SER265 3.8 23.7 1.0
CAJ B:68Q401 3.9 30.2 1.0
CAR B:68Q401 4.0 31.9 1.0
CB B:ALA268 4.0 22.6 1.0
CB B:SER265 4.2 25.0 1.0
N B:SER265 4.3 24.0 1.0
O B:ILE264 4.4 26.1 1.0
CAI B:68Q401 4.5 31.0 1.0
CG2 B:ILE264 4.5 30.1 1.0
C B:ILE264 4.6 25.2 1.0
CB B:PRO210 4.9 33.8 1.0
C B:SER265 4.9 23.3 1.0
NAN B:68Q401 5.0 30.3 1.0

Chlorine binding site 4 out of 8 in 5i7a

Go back to Chlorine Binding Sites List in 5i7a
Chlorine binding site 4 out of 8 in the Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:35.9
occ:1.00
 CL2 B:68Q401 0.0 35.9 1.0
CAS B:68Q401 1.8 31.4 1.0
CAT B:68Q401 2.7 32.2 1.0
CAJ B:68Q401 2.7 30.2 1.0
CL1 B:68Q401 3.1 41.9 1.0
C B:GLU209 3.3 28.2 1.0
CB B:ALA268 3.3 22.6 1.0
N B:PRO210 3.4 31.4 1.0
CA B:GLU209 3.5 28.6 1.0
N B:GLU209 3.7 25.0 1.0
O B:GLU209 3.7 30.0 1.0
CD B:PRO210 3.8 31.8 1.0
C B:ALA208 3.9 24.9 1.0
O B:ALA208 3.9 24.2 1.0
CAK B:68Q401 4.0 31.4 1.0
CAI B:68Q401 4.0 31.0 1.0
CA B:PRO210 4.0 33.8 1.0
CB B:ALA208 4.4 25.0 1.0
CAR B:68Q401 4.5 31.9 1.0
CB B:PRO210 4.6 33.8 1.0
CG B:PRO210 4.6 34.1 1.0
CA B:ALA208 4.7 24.5 1.0
CA B:ALA268 4.8 22.2 1.0
CB B:VAL242 5.0 30.4 1.0

Chlorine binding site 5 out of 8 in 5i7a

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Chlorine binding site 5 out of 8 in the Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid] within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:57.1
occ:1.00
 CL1 C:68Q401 0.0 57.1 1.0
CAT C:68Q401 1.7 50.0 1.0
CAK C:68Q401 2.7 46.1 1.0
CAS C:68Q401 2.7 51.1 1.0
CL2 C:68Q401 3.0 53.1 1.0
CA C:SER265 3.9 36.2 1.0
CAR C:68Q401 4.0 44.2 1.0
CAJ C:68Q401 4.0 48.2 1.0
CB C:ALA268 4.2 43.3 1.0
CB C:SER265 4.2 37.4 1.0
N C:SER265 4.3 37.8 1.0
CAI C:68Q401 4.5 47.6 1.0
CB C:PRO210 4.6 53.9 1.0
C C:ILE264 4.7 38.3 1.0
CG2 C:ILE264 4.7 41.9 1.0
O C:ILE264 4.8 38.1 1.0
NAN C:68Q401 5.0 41.8 1.0
C C:SER265 5.0 35.6 1.0

Chlorine binding site 6 out of 8 in 5i7a

Go back to Chlorine Binding Sites List in 5i7a
Chlorine binding site 6 out of 8 in the Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid] within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:53.1
occ:1.00
 CL2 C:68Q401 0.0 53.1 1.0
CAS C:68Q401 1.7 51.1 1.0
CAT C:68Q401 2.7 50.0 1.0
CAJ C:68Q401 2.8 48.2 1.0
CL1 C:68Q401 3.0 57.1 1.0
CB C:ALA268 3.2 43.3 1.0
N C:PRO210 3.4 49.7 1.0
C C:GLU209 3.4 49.1 1.0
CA C:GLU209 3.5 48.6 1.0
CD C:PRO210 3.7 48.8 1.0
N C:GLU209 3.8 45.5 1.0
O C:GLU209 3.9 49.5 1.0
C C:ALA208 4.0 43.5 1.0
CAK C:68Q401 4.0 46.1 1.0
CA C:PRO210 4.0 53.5 1.0
CAI C:68Q401 4.1 47.6 1.0
O C:ALA208 4.1 43.6 1.0
CB C:PRO210 4.4 53.9 1.0
CB C:ALA208 4.5 46.9 1.0
CAR C:68Q401 4.6 44.2 1.0
CG C:PRO210 4.6 50.8 1.0
CA C:ALA268 4.7 42.4 1.0
CA C:ALA208 4.9 45.5 1.0
O C:SER265 4.9 38.5 1.0
CB C:GLU209 5.0 55.4 1.0

Chlorine binding site 7 out of 8 in 5i7a

Go back to Chlorine Binding Sites List in 5i7a
Chlorine binding site 7 out of 8 in the Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid] within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:35.3
occ:1.00
 CL1 D:68Q401 0.0 35.3 1.0
CAT D:68Q401 1.8 29.7 1.0
CAS D:68Q401 2.7 29.0 1.0
CAK D:68Q401 2.8 27.5 1.0
CL2 D:68Q401 3.0 30.6 1.0
CD2 D:LEU219 3.2 45.6 1.0
CG D:LEU219 3.6 43.8 1.0
CA D:SER265 3.9 24.1 1.0
CAJ D:68Q401 4.0 27.8 1.0
CG D:PRO210 4.0 36.1 1.0
CAR D:68Q401 4.1 27.5 1.0
CB D:ALA323 4.2 35.6 1.0
CB D:ALA268 4.3 24.0 1.0
CD1 D:LEU219 4.3 43.7 1.0
N D:SER265 4.3 23.9 1.0
CB D:SER265 4.4 25.5 1.0
CAI D:68Q401 4.6 27.6 1.0
CD D:PRO210 4.7 33.1 1.0
O D:ILE264 4.7 23.4 1.0
CG2 D:ILE264 4.7 31.5 1.0
C D:ILE264 4.7 24.3 1.0
CB D:PRO210 4.8 35.4 1.0
CB D:LEU219 4.9 43.0 1.0

Chlorine binding site 8 out of 8 in 5i7a

Go back to Chlorine Binding Sites List in 5i7a
Chlorine binding site 8 out of 8 in the Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 1 [3-(3-(3,4-Dichlorophenyl)Ureido)Benzoic Acid] within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:30.6
occ:1.00
 CL2 D:68Q401 0.0 30.6 1.0
CAS D:68Q401 1.8 29.0 1.0
CAT D:68Q401 2.7 29.7 1.0
CAJ D:68Q401 2.8 27.8 1.0
CL1 D:68Q401 3.0 35.3 1.0
CB D:ALA268 3.4 24.0 1.0
C D:GLU209 3.4 28.9 1.0
CA D:GLU209 3.5 28.2 1.0
N D:PRO210 3.6 31.1 1.0
O D:ALA208 3.7 25.5 1.0
CD D:PRO210 3.7 33.1 1.0
N D:GLU209 3.7 26.9 1.0
C D:ALA208 3.7 26.3 1.0
O D:GLU209 3.9 27.1 1.0
CAK D:68Q401 4.0 27.5 1.0
CG D:PRO210 4.1 36.1 1.0
CAI D:68Q401 4.1 27.6 1.0
CB D:ALA208 4.2 27.1 1.0
CA D:PRO210 4.3 35.5 1.0
CAR D:68Q401 4.6 27.5 1.0
CA D:ALA208 4.6 26.1 1.0
CB D:PRO210 4.8 35.4 1.0
CA D:ALA268 4.8 24.4 1.0
CD2 D:LEU219 4.8 45.6 1.0
O D:SER265 4.9 22.5 1.0
CB D:GLU209 4.9 30.0 1.0

Reference:

K.Brunner, S.Maric, R.S.Reshma, H.Almqvist, B.Seashore-Ludlow, A.L.Gustavsson, O.Poyraz, P.Yogeeswari, T.Lundback, M.Vallin, D.Sriram, R.Schnell, G.Schneider. Inhibitors of the Cysteine Synthase Cysm with Antibacterial Potency Against Dormant Mycobacterium Tuberculosis. J.Med.Chem. V. 59 6848 2016.
ISSN: ISSN 0022-2623
PubMed: 27379713
DOI: 10.1021/ACS.JMEDCHEM.6B00674
Page generated: Fri Jul 26 09:12:24 2024

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