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Chlorine in PDB 4qo8: Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104

Enzymatic activity of Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104

All present enzymatic activity of Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104:
1.1.1.27;

Protein crystallography data

The structure of Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104, PDB code: 4qo8 was solved by C.Eigenbrot, M.Ultsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.41 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.352, 81.257, 120.760, 90.00, 117.61, 90.00
R / Rfree (%) 15.7 / 20.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104 (pdb code 4qo8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104, PDB code: 4qo8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 4qo8

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Chlorine binding site 1 out of 9 in the Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl804

b:50.3
occ:1.00
 CL1 A:36U804 0.0 50.3 1.0
C11 A:36U804 1.7 43.2 1.0
C10 A:36U804 2.7 43.3 1.0
C6 A:36U804 2.8 41.9 1.0
NH2 A:ARG168 3.0 45.2 1.0
S5 A:36U804 3.3 42.0 1.0
OD1 A:ASP165 3.3 39.6 1.0
CG A:ASP165 3.4 39.4 1.0
CA A:ASP165 3.8 39.0 1.0
OD2 A:ASP165 3.8 39.6 1.0
CE1 A:HIS192 3.9 42.0 1.0
CB A:ASP165 4.0 38.5 1.0
C9 A:36U804 4.0 41.6 1.0
C7 A:36U804 4.0 39.3 1.0
N A:ASP165 4.1 32.5 1.0
O A:HOH920 4.1 33.7 1.0
CD A:ARG168 4.2 39.6 1.0
CZ A:ARG168 4.2 46.5 1.0
CG1 A:VAL233 4.2 44.5 1.0
O A:VAL233 4.5 47.9 1.0
ND1 A:HIS192 4.5 38.3 1.0
C8 A:36U804 4.5 42.0 1.0
C A:LEU164 4.6 36.0 1.0
CD2 A:LEU164 4.6 34.7 1.0
NE A:ARG168 4.7 40.8 1.0
CG A:LEU164 4.7 36.2 1.0
CB A:ALA237 4.7 44.3 1.0
NE2 A:HIS192 4.8 42.1 1.0
O A:LEU164 4.8 35.5 1.0
C4 A:36U804 4.9 43.3 1.0

Chlorine binding site 2 out of 9 in 4qo8

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Chlorine binding site 2 out of 9 in the Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl804

b:61.7
occ:1.00
 CL2 A:36U804 0.0 61.7 1.0
C17 A:36U804 1.7 64.1 1.0
C19 A:36U804 2.7 64.1 1.0
C16 A:36U804 2.8 58.6 1.0
O A:HOH931 3.2 36.6 1.0
C15 A:36U804 3.2 52.7 1.0
C14 A:36U804 3.3 47.2 1.0
C3 A:36U804 3.3 46.4 1.0
C6N A:NAI801 3.7 40.0 1.0
O A:HOH1043 3.7 50.2 1.0
O2D A:NAI801 3.8 44.4 1.0
C2D A:NAI801 3.9 41.3 1.0
C20 A:36U804 4.0 58.7 1.0
CD1 A:ILE241 4.0 39.6 1.0
C22 A:36U804 4.0 62.6 1.0
C5N A:NAI801 4.1 39.4 1.0
C13 A:36U804 4.5 46.6 1.0
C2 A:36U804 4.5 45.6 1.0
C21 A:36U804 4.5 59.3 1.0
OG1 A:THR247 4.5 49.5 1.0
N1N A:NAI801 4.6 41.0 1.0
CG1 A:ILE241 4.8 42.5 1.0
O2N A:NAI801 4.8 37.4 1.0
N A:THR247 4.8 34.0 1.0
C1D A:NAI801 4.9 39.7 1.0
O5D A:NAI801 5.0 32.1 1.0
C4 A:36U804 5.0 43.3 1.0

Chlorine binding site 3 out of 9 in 4qo8

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Chlorine binding site 3 out of 9 in the Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl804

b:58.3
occ:1.00
 CL3 A:36U804 0.0 58.3 1.0
C22 A:36U804 1.7 62.6 1.0
C21 A:36U804 2.7 59.3 1.0
C16 A:36U804 2.7 58.6 1.0
C15 A:36U804 2.9 52.7 1.0
CE1 A:TYR238 3.5 49.0 1.0
CD1 A:TYR238 3.6 45.0 1.0
C20 A:36U804 4.0 58.7 1.0
C17 A:36U804 4.0 64.1 1.0
C3 A:36U804 4.0 46.4 1.0
C14 A:36U804 4.0 47.2 1.0
CZ A:TYR238 4.2 50.9 1.0
CG1 A:ILE241 4.3 42.5 1.0
C19 A:36U804 4.5 64.1 1.0
CG A:TYR238 4.5 43.5 1.0
OH A:TYR238 4.7 53.5 1.0
C2 A:36U804 4.7 45.6 1.0
C13 A:36U804 4.8 46.6 1.0
C7 A:36U804 5.0 39.3 1.0
CE2 A:TYR238 5.0 48.1 1.0

Chlorine binding site 4 out of 9 in 4qo8

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Chlorine binding site 4 out of 9 in the Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl804

b:52.1
occ:1.00
 CL1 C:36U804 0.0 52.1 1.0
C11 C:36U804 1.7 41.6 1.0
C10 C:36U804 2.7 46.5 1.0
C6 C:36U804 2.7 42.5 1.0
S5 C:36U804 3.2 48.6 1.0
NH2 C:ARG168 3.2 42.8 1.0
CG C:ASP165 3.4 42.3 1.0
OD1 C:ASP165 3.4 43.2 1.0
CA C:ASP165 3.6 33.5 1.0
OD2 C:ASP165 3.6 48.1 1.0
CE1 C:HIS192 3.9 42.5 1.0
N C:ASP165 3.9 37.1 1.0
CB C:ASP165 3.9 36.5 1.0
C9 C:36U804 4.0 50.9 1.0
C7 C:36U804 4.0 45.2 1.0
O C:HOH1036 4.1 51.7 1.0
CG1 C:VAL233 4.2 40.6 1.0
CD C:ARG168 4.3 33.5 1.0
CZ C:ARG168 4.4 41.1 1.0
C C:LEU164 4.4 35.5 1.0
ND1 C:HIS192 4.4 40.7 1.0
CG C:LEU164 4.5 36.5 1.0
C8 C:36U804 4.5 49.7 1.0
O C:LEU164 4.7 32.5 1.0
O C:VAL233 4.8 53.5 1.0
NE C:ARG168 4.8 35.1 1.0
NE2 C:HIS192 4.8 43.6 1.0
CD2 C:LEU164 4.8 41.0 1.0
CB C:LEU164 4.8 36.5 1.0
C4 C:36U804 4.9 49.4 1.0
CB C:ALA237 4.9 48.0 1.0
C C:ASP165 5.0 34.1 1.0

Chlorine binding site 5 out of 9 in 4qo8

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Chlorine binding site 5 out of 9 in the Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl804

b:64.0
occ:1.00
 CL2 C:36U804 0.0 64.0 1.0
C17 C:36U804 1.7 54.2 1.0
C19 C:36U804 2.7 53.9 1.0
C16 C:36U804 2.7 57.0 1.0
C15 C:36U804 3.2 53.2 1.0
C3 C:36U804 3.2 49.3 1.0
C14 C:36U804 3.2 47.7 1.0
C6N C:NAI801 3.4 41.9 1.0
O2D C:NAI801 3.7 47.6 1.0
C2D C:NAI801 3.8 44.8 1.0
C5N C:NAI801 3.9 44.0 1.0
C20 C:36U804 4.0 54.9 1.0
C22 C:36U804 4.0 57.4 1.0
CD1 C:ILE241 4.2 50.5 1.0
N1N C:NAI801 4.3 41.9 1.0
CG2 C:THR247 4.4 40.6 1.0
C2 C:36U804 4.4 48.2 1.0
C13 C:36U804 4.4 49.9 1.0
C21 C:36U804 4.5 57.4 1.0
O2N C:NAI801 4.6 37.7 1.0
C1D C:NAI801 4.6 40.3 1.0
C4 C:36U804 4.9 49.4 1.0
O5D C:NAI801 4.9 40.3 1.0
C3D C:NAI801 4.9 43.9 1.0

Chlorine binding site 6 out of 9 in 4qo8

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Chlorine binding site 6 out of 9 in the Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl804

b:60.1
occ:1.00
 CL3 C:36U804 0.0 60.1 1.0
C22 C:36U804 1.7 57.4 1.0
C16 C:36U804 2.7 57.0 1.0
C21 C:36U804 2.7 57.4 1.0
C15 C:36U804 2.9 53.2 1.0
CE2 C:TYR238 3.3 60.2 1.0
CD2 C:TYR238 3.5 56.4 1.0
C3 C:36U804 4.0 49.3 1.0
C17 C:36U804 4.0 54.2 1.0
C20 C:36U804 4.0 54.9 1.0
C14 C:36U804 4.0 47.7 1.0
CZ C:TYR238 4.1 60.6 1.0
CG C:TYR238 4.5 52.9 1.0
C19 C:36U804 4.5 53.9 1.0
CG1 C:ILE241 4.5 49.5 1.0
OH C:TYR238 4.6 64.7 1.0
C2 C:36U804 4.7 48.2 1.0
C13 C:36U804 4.8 49.9 1.0
C7 C:36U804 4.9 45.2 1.0
CE1 C:TYR238 5.0 57.2 1.0
O C:HOH1031 5.0 53.7 1.0
CA C:TYR238 5.0 45.4 1.0

Chlorine binding site 7 out of 9 in 4qo8

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Chlorine binding site 7 out of 9 in the Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl803

b:43.9
occ:1.00
 CL1 D:36U803 0.0 43.9 1.0
C11 D:36U803 1.8 50.4 1.0
C10 D:36U803 2.7 51.9 1.0
C6 D:36U803 2.7 50.3 1.0
NH2 D:ARG168 3.0 39.6 1.0
S5 D:36U803 3.2 42.0 1.0
CG D:ASP165 3.3 29.4 1.0
OD1 D:ASP165 3.4 31.5 1.0
OD2 D:ASP165 3.7 33.1 1.0
CA D:ASP165 3.7 26.4 1.0
CB D:ASP165 3.8 23.1 1.0
CE1 D:HIS192 3.9 35.1 1.0
N D:ASP165 3.9 24.2 1.0
C9 D:36U803 4.0 49.6 1.0
C7 D:36U803 4.0 50.2 1.0
O D:HOH941 4.2 38.9 1.0
CZ D:ARG168 4.2 38.6 1.0
CG1 D:VAL233 4.3 34.5 1.0
CD D:ARG168 4.3 32.3 1.0
ND1 D:HIS192 4.5 33.0 1.0
C D:LEU164 4.5 26.4 1.0
O D:VAL233 4.5 45.6 1.0
C8 D:36U803 4.5 49.4 1.0
CG D:LEU164 4.6 33.4 1.0
NE D:ARG168 4.7 33.7 1.0
CB D:ALA237 4.7 42.4 1.0
CD2 D:LEU164 4.8 31.8 1.0
O D:LEU164 4.8 24.5 1.0
C4 D:36U803 4.9 37.1 1.0
NE2 D:HIS192 4.9 34.8 1.0
CB D:LEU164 5.0 31.0 1.0

Chlorine binding site 8 out of 9 in 4qo8

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Chlorine binding site 8 out of 9 in the Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl803

b:57.5
occ:1.00
 CL2 D:36U803 0.0 57.5 1.0
C17 D:36U803 1.7 55.9 1.0
C19 D:36U803 2.7 56.4 1.0
C16 D:36U803 2.8 50.9 1.0
O D:HOH1015 3.0 45.7 1.0
C15 D:36U803 3.2 46.3 1.0
C14 D:36U803 3.3 44.4 1.0
C3 D:36U803 3.3 40.1 1.0
O D:HOH1051 3.6 52.6 1.0
C6N D:NAI801 3.6 47.0 1.0
O2D D:NAI801 3.8 43.1 1.0
C2D D:NAI801 3.9 44.2 1.0
C20 D:36U803 4.0 56.3 1.0
C22 D:36U803 4.0 55.5 1.0
CD1 D:ILE241 4.0 51.0 1.0
C5N D:NAI801 4.1 45.0 1.0
OG1 D:THR247 4.5 52.7 1.0
C21 D:36U803 4.5 55.4 1.0
C13 D:36U803 4.5 48.1 1.0
N1N D:NAI801 4.5 45.5 1.0
C2 D:36U803 4.6 39.9 1.0
O2N D:NAI801 4.6 41.1 1.0
C1D D:NAI801 4.8 45.8 1.0
N D:THR247 4.8 40.4 1.0
CG1 D:ILE241 4.9 49.3 1.0
O5D D:NAI801 5.0 41.9 1.0

Chlorine binding site 9 out of 9 in 4qo8

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Chlorine binding site 9 out of 9 in the Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Lactate Dehydrogenase A in Complex with Substituted 3-Hydroxy-2- Mercaptocyclohex-2-Enone Compound 104 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl803

b:69.3
occ:1.00
 CL3 D:36U803 0.0 69.3 1.0
C22 D:36U803 1.7 55.5 1.0
C16 D:36U803 2.7 50.9 1.0
C21 D:36U803 2.7 55.4 1.0
C15 D:36U803 2.9 46.3 1.0
CE1 D:TYR238 3.4 50.7 1.0
CD1 D:TYR238 3.7 45.5 1.0
C3 D:36U803 4.0 40.1 1.0
C17 D:36U803 4.0 55.9 1.0
C14 D:36U803 4.0 44.4 1.0
C20 D:36U803 4.0 56.3 1.0
CZ D:TYR238 4.0 50.9 1.0
OH D:TYR238 4.5 55.6 1.0
CG D:TYR238 4.5 41.0 1.0
C19 D:36U803 4.5 56.4 1.0
CG1 D:ILE241 4.5 49.3 1.0
C2 D:36U803 4.7 39.9 1.0
C13 D:36U803 4.7 48.1 1.0
CE2 D:TYR238 4.8 40.7 1.0
C7 D:36U803 4.8 50.2 1.0
CD2 D:TYR238 5.0 41.2 1.0
C4 D:36U803 5.0 37.1 1.0

Reference:

P.S.Dragovich, B.P.Fauber, J.Boggs, J.Chen, L.B.Corson, C.Z.Ding, C.Eigenbrot, H.Ge, A.M.Giannetti, T.Hunsaker, S.Labadie, C.Li, Y.Liu, Y.Liu, S.Ma, S.Malek, D.Peterson, K.E.Pitts, H.E.Purkey, K.Robarge, L.Salphati, S.Sideris, M.Ultsch, E.Vanderporten, J.Wang, B.Wei, Q.Xu, I.Yen, Q.Yue, H.Zhang, X.Zhang, A.Zhou. Identification of Substituted 3-Hydroxy-2-Mercaptocyclohex-2-Enones As Potent Inhibitors of Human Lactate Dehydrogenase. Bioorg.Med.Chem.Lett. V. 24 3764 2014.
ISSN: ISSN 0960-894X
PubMed: 25037916
DOI: 10.1016/J.BMCL.2014.06.076
Page generated: Fri Jul 11 20:52:56 2025

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