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Chlorine in PDB 4r69: Lactate Dehydrogenase in Complex with Inhibitor Compound 13

Enzymatic activity of Lactate Dehydrogenase in Complex with Inhibitor Compound 13

All present enzymatic activity of Lactate Dehydrogenase in Complex with Inhibitor Compound 13:
1.1.1.27;

Protein crystallography data

The structure of Lactate Dehydrogenase in Complex with Inhibitor Compound 13, PDB code: 4r69 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) 38.83 / 3.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.007, 80.682, 101.983, 90.00, 96.49, 90.00
R / Rfree (%) 19 / 22.8

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Lactate Dehydrogenase in Complex with Inhibitor Compound 13 (pdb code 4r69). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Lactate Dehydrogenase in Complex with Inhibitor Compound 13, PDB code: 4r69:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 4r69

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Chlorine binding site 1 out of 12 in the Lactate Dehydrogenase in Complex with Inhibitor Compound 13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lactate Dehydrogenase in Complex with Inhibitor Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:55.6
occ:1.00
 CL1 A:W13403 0.0 55.6 1.0
C2 A:W13403 1.7 56.6 1.0
C3 A:W13403 2.7 58.0 1.0
C15 A:W13403 2.8 55.4 1.0
C16 A:W13403 3.2 52.3 1.0
C17 A:W13403 3.5 51.2 1.0
C30 A:W13403 3.5 50.2 1.0
CG A:ARG98 3.6 51.5 1.0
C6N A:NAI402 3.8 30.2 1.0
C2D A:NAI402 4.0 34.9 1.0
O2D A:NAI402 4.0 35.5 1.0
CD1 A:ILE241 4.0 46.7 1.0
C4 A:W13403 4.0 59.0 1.0
C13 A:W13403 4.1 56.4 1.0
CB A:ARG98 4.2 46.9 1.0
CG2 A:THR247 4.3 50.4 1.0
C5N A:NAI402 4.4 29.4 1.0
CA A:ARG98 4.5 48.1 1.0
O1N A:NAI402 4.5 41.2 1.0
CD A:ARG98 4.6 57.0 1.0
C5 A:W13403 4.6 59.3 1.0
C18 A:W13403 4.7 50.4 1.0
C28 A:W13403 4.7 49.8 1.0
N1N A:NAI402 4.8 31.7 1.0
O5D A:NAI402 4.9 39.6 1.0
C1D A:NAI402 4.9 34.3 1.0
O A:ARG98 4.9 51.2 1.0
N A:THR247 4.9 43.1 1.0
CG1 A:ILE241 4.9 40.2 1.0

Chlorine binding site 2 out of 12 in 4r69

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Chlorine binding site 2 out of 12 in the Lactate Dehydrogenase in Complex with Inhibitor Compound 13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lactate Dehydrogenase in Complex with Inhibitor Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:54.2
occ:1.00
 CL14 A:W13403 0.0 54.2 1.0
C13 A:W13403 1.7 56.4 1.0
C5 A:W13403 2.7 59.3 1.0
C15 A:W13403 2.7 55.4 1.0
N6 A:W13403 2.9 61.7 1.0
C16 A:W13403 2.9 52.3 1.0
CE1 A:TYR238 3.3 42.4 1.0
CD1 A:TYR238 3.6 41.3 1.0
C30 A:W13403 3.9 50.2 1.0
CZ A:TYR238 3.9 48.9 1.0
C17 A:W13403 4.0 51.2 1.0
C4 A:W13403 4.0 59.0 1.0
C2 A:W13403 4.0 56.6 1.0
C7 A:W13403 4.2 63.2 1.0
CG1 A:ILE241 4.3 40.2 1.0
CG A:TYR238 4.4 39.4 1.0
OH A:TYR238 4.4 50.0 1.0
C3 A:W13403 4.5 58.0 1.0
C28 A:W13403 4.6 49.8 1.0
C12 A:W13403 4.6 64.0 1.0
C18 A:W13403 4.6 50.4 1.0
CE2 A:TYR238 4.7 40.9 1.0
C27 A:W13403 4.7 46.4 1.0
C19 A:W13403 4.8 49.4 1.0
CD2 A:TYR238 4.9 39.9 1.0
CA A:TYR238 5.0 38.4 1.0
O A:ALA237 5.0 44.4 1.0

Chlorine binding site 3 out of 12 in 4r69

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Chlorine binding site 3 out of 12 in the Lactate Dehydrogenase in Complex with Inhibitor Compound 13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lactate Dehydrogenase in Complex with Inhibitor Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:47.9
occ:1.00
 CL23 A:W13403 0.0 47.9 1.0
C22 A:W13403 1.7 47.9 1.0
C24 A:W13403 2.7 47.0 1.0
C21 A:W13403 2.7 47.7 1.0
NH2 A:ARG168 3.1 27.0 1.0
S20 A:W13403 3.2 48.7 1.0
CG A:ASP165 3.5 42.4 1.0
OD1 A:ASP165 3.6 41.7 1.0
OD2 A:ASP165 3.6 50.3 1.0
CA A:ASP165 3.8 30.1 1.0
N A:ASP165 3.9 30.4 1.0
CE1 A:HIS192 4.0 44.0 1.0
C25 A:W13403 4.0 45.7 1.0
C27 A:W13403 4.0 46.4 1.0
CD A:ARG168 4.1 30.8 1.0
CB A:ASP165 4.1 32.0 1.0
CG A:LEU164 4.2 32.8 1.0
CG1 A:VAL233 4.2 45.7 1.0
CZ A:ARG168 4.2 43.0 1.0
CD2 A:LEU164 4.3 35.2 1.0
C A:LEU164 4.3 33.6 1.0
ND1 A:HIS192 4.4 44.9 1.0
C26 A:W13403 4.5 45.6 1.0
O A:LEU164 4.6 33.0 1.0
NE A:ARG168 4.6 34.7 1.0
O A:VAL233 4.6 47.8 1.0
CB A:LEU164 4.7 28.9 1.0
CB A:ALA237 4.8 43.9 1.0
C19 A:W13403 4.8 49.4 1.0

Chlorine binding site 4 out of 12 in 4r69

Go back to Chlorine Binding Sites List in 4r69
Chlorine binding site 4 out of 12 in the Lactate Dehydrogenase in Complex with Inhibitor Compound 13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lactate Dehydrogenase in Complex with Inhibitor Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:41.7
occ:1.00
 CL1 B:W13403 0.0 41.7 1.0
C2 B:W13403 1.7 40.0 1.0
C3 B:W13403 2.7 38.3 1.0
C15 B:W13403 2.7 39.7 1.0
C16 B:W13403 3.2 37.5 1.0
C30 B:W13403 3.5 35.2 1.0
CG B:ARG98 3.5 55.0 1.0
C17 B:W13403 3.6 36.3 1.0
CD1 B:ILE241 3.7 48.7 1.0
C6N B:NAI402 4.0 37.2 1.0
C4 B:W13403 4.0 37.9 1.0
C13 B:W13403 4.0 40.5 1.0
O2D B:NAI402 4.1 35.3 1.0
C2D B:NAI402 4.1 34.3 1.0
OG1 B:THR247 4.2 54.0 1.0
CB B:ARG98 4.4 53.7 1.0
C5N B:NAI402 4.4 36.6 1.0
CD B:ARG98 4.4 53.2 1.0
C5 B:W13403 4.6 38.4 1.0
O1N B:NAI402 4.6 36.6 1.0
CG1 B:ILE241 4.6 40.4 1.0
CA B:ARG98 4.7 55.2 1.0
N B:THR247 4.7 38.6 1.0
C28 B:W13403 4.8 34.0 1.0
N1N B:NAI402 4.9 36.5 1.0
C18 B:W13403 4.9 34.9 1.0
C1D B:NAI402 5.0 35.1 1.0

Chlorine binding site 5 out of 12 in 4r69

Go back to Chlorine Binding Sites List in 4r69
Chlorine binding site 5 out of 12 in the Lactate Dehydrogenase in Complex with Inhibitor Compound 13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Lactate Dehydrogenase in Complex with Inhibitor Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:43.8
occ:1.00
 CL14 B:W13403 0.0 43.8 1.0
C13 B:W13403 1.7 40.5 1.0
C5 B:W13403 2.7 38.4 1.0
C15 B:W13403 2.7 39.7 1.0
N6 B:W13403 2.8 37.5 1.0
C16 B:W13403 2.9 37.5 1.0
CE1 B:TYR238 3.4 45.0 1.0
C17 B:W13403 3.6 36.3 1.0
CD1 B:TYR238 3.7 43.6 1.0
CZ B:TYR238 3.9 50.2 1.0
C30 B:W13403 3.9 35.2 1.0
C4 B:W13403 4.0 37.9 1.0
C2 B:W13403 4.0 40.0 1.0
C18 B:W13403 4.1 34.9 1.0
C7 B:W13403 4.2 36.2 1.0
C27 B:W13403 4.3 36.3 1.0
OH B:TYR238 4.3 51.0 1.0
C28 B:W13403 4.4 34.0 1.0
CG B:TYR238 4.4 41.2 1.0
C19 B:W13403 4.5 34.7 1.0
CG1 B:ILE241 4.5 40.4 1.0
C3 B:W13403 4.5 38.3 1.0
CE2 B:TYR238 4.5 42.1 1.0
C26 B:W13403 4.7 36.4 1.0
O31 B:W13403 4.8 33.6 1.0
CD2 B:TYR238 4.8 41.4 1.0
O B:ALA237 4.9 44.5 1.0
C B:ALA237 4.9 44.7 1.0
C12 B:W13403 5.0 36.8 1.0
N B:TYR238 5.0 40.4 1.0
CA B:TYR238 5.0 39.3 1.0

Chlorine binding site 6 out of 12 in 4r69

Go back to Chlorine Binding Sites List in 4r69
Chlorine binding site 6 out of 12 in the Lactate Dehydrogenase in Complex with Inhibitor Compound 13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Lactate Dehydrogenase in Complex with Inhibitor Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:38.6
occ:1.00
 CL23 B:W13403 0.0 38.6 1.0
C22 B:W13403 1.7 38.5 1.0
C24 B:W13403 2.7 38.8 1.0
C21 B:W13403 2.7 37.0 1.0
S20 B:W13403 3.2 35.8 1.0
NH2 B:ARG168 3.2 23.5 1.0
CG B:ASP165 3.4 41.6 1.0
OD1 B:ASP165 3.5 42.2 1.0
OD2 B:ASP165 3.5 46.9 1.0
CA B:ASP165 3.6 29.0 1.0
N B:ASP165 3.8 29.0 1.0
CB B:ASP165 3.9 31.2 1.0
C25 B:W13403 4.0 37.5 1.0
C27 B:W13403 4.0 36.3 1.0
CE1 B:HIS192 4.1 40.6 1.0
CG1 B:VAL233 4.1 37.3 1.0
CD B:ARG168 4.1 30.9 1.0
CG B:LEU164 4.2 33.2 1.0
C B:LEU164 4.2 33.3 1.0
CZ B:ARG168 4.3 43.8 1.0
CD2 B:LEU164 4.4 34.3 1.0
ND1 B:HIS192 4.4 41.4 1.0
O B:LEU164 4.5 33.3 1.0
C26 B:W13403 4.6 36.4 1.0
O B:VAL233 4.6 39.6 1.0
CB B:LEU164 4.6 29.8 1.0
NE B:ARG168 4.7 36.6 1.0
CB B:ALA237 4.8 41.4 1.0
C19 B:W13403 4.9 34.7 1.0

Chlorine binding site 7 out of 12 in 4r69

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Chlorine binding site 7 out of 12 in the Lactate Dehydrogenase in Complex with Inhibitor Compound 13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Lactate Dehydrogenase in Complex with Inhibitor Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:42.2
occ:1.00
 CL1 C:W13403 0.0 42.2 1.0
C2 C:W13403 1.7 40.8 1.0
C3 C:W13403 2.7 40.4 1.0
C15 C:W13403 2.8 39.5 1.0
C16 C:W13403 3.2 35.8 1.0
C30 C:W13403 3.4 34.7 1.0
CD1 C:ILE241 3.5 43.8 1.0
C17 C:W13403 3.6 35.4 1.0
CG C:ARG98 3.7 54.8 1.0
CD C:ARG98 3.9 56.4 1.0
C4 C:W13403 4.0 41.2 1.0
CB C:ARG98 4.0 54.2 1.0
C13 C:W13403 4.0 41.9 1.0
C6N C:NAI402 4.3 39.7 1.0
CG2 C:THR247 4.4 44.4 1.0
O2D C:NAI402 4.4 40.9 1.0
CG1 C:ILE241 4.4 38.0 1.0
C2D C:NAI402 4.5 40.2 1.0
CA C:ARG98 4.6 56.3 1.0
C5 C:W13403 4.6 43.0 1.0
NE C:ARG98 4.6 59.2 1.0
N C:THR247 4.7 35.3 1.0
C5N C:NAI402 4.8 40.7 1.0
O1N C:NAI402 4.8 40.1 1.0
C28 C:W13403 4.8 35.4 1.0
C18 C:W13403 4.9 35.5 1.0
CA C:TYR246 4.9 36.3 1.0

Chlorine binding site 8 out of 12 in 4r69

Go back to Chlorine Binding Sites List in 4r69
Chlorine binding site 8 out of 12 in the Lactate Dehydrogenase in Complex with Inhibitor Compound 13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Lactate Dehydrogenase in Complex with Inhibitor Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:44.6
occ:1.00
 CL14 C:W13403 0.0 44.6 1.0
C13 C:W13403 1.7 41.9 1.0
C15 C:W13403 2.7 39.5 1.0
C5 C:W13403 2.7 43.0 1.0
N6 C:W13403 2.9 46.1 1.0
C16 C:W13403 2.9 35.8 1.0
CE1 C:TYR238 3.2 44.6 1.0
CD1 C:TYR238 3.7 43.8 1.0
CZ C:TYR238 3.7 48.4 1.0
C17 C:W13403 3.8 35.4 1.0
C30 C:W13403 4.0 34.7 1.0
C4 C:W13403 4.0 41.2 1.0
C2 C:W13403 4.0 40.8 1.0
OH C:TYR238 4.1 45.5 1.0
C18 C:W13403 4.3 35.5 1.0
C27 C:W13403 4.3 35.3 1.0
C7 C:W13403 4.3 48.7 1.0
C3 C:W13403 4.5 40.4 1.0
CG C:TYR238 4.5 41.6 1.0
CE2 C:TYR238 4.5 42.8 1.0
C28 C:W13403 4.5 35.4 1.0
C26 C:W13403 4.6 35.8 1.0
C19 C:W13403 4.6 35.0 1.0
CG1 C:ILE241 4.8 38.0 1.0
CD2 C:TYR238 4.8 42.0 1.0
O31 C:W13403 4.9 35.7 1.0

Chlorine binding site 9 out of 12 in 4r69

Go back to Chlorine Binding Sites List in 4r69
Chlorine binding site 9 out of 12 in the Lactate Dehydrogenase in Complex with Inhibitor Compound 13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Lactate Dehydrogenase in Complex with Inhibitor Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:40.1
occ:1.00
 CL23 C:W13403 0.0 40.1 1.0
C22 C:W13403 1.7 37.5 1.0
C24 C:W13403 2.7 36.6 1.0
C21 C:W13403 2.8 35.5 1.0
S20 C:W13403 3.2 34.0 1.0
NH2 C:ARG168 3.3 38.4 1.0
CG C:ASP165 3.4 33.2 1.0
OD2 C:ASP165 3.5 34.5 1.0
OD1 C:ASP165 3.7 32.9 1.0
CA C:ASP165 3.8 28.7 1.0
C25 C:W13403 4.0 35.7 1.0
CB C:ASP165 4.0 30.0 1.0
CG1 C:VAL233 4.0 42.1 1.0
C27 C:W13403 4.0 35.3 1.0
N C:ASP165 4.1 29.5 1.0
CE1 C:HIS192 4.1 41.1 1.0
CD C:ARG168 4.2 37.1 1.0
CZ C:ARG168 4.4 56.5 1.0
ND1 C:HIS192 4.5 42.0 1.0
O C:VAL233 4.5 44.5 1.0
CG C:LEU164 4.5 35.4 1.0
C26 C:W13403 4.5 35.8 1.0
C C:LEU164 4.6 34.2 1.0
CD2 C:LEU164 4.6 38.1 1.0
CB C:ALA237 4.7 42.6 1.0
NE C:ARG168 4.8 45.3 1.0
O C:LEU164 4.8 34.0 1.0
C19 C:W13403 4.9 35.0 1.0
CB C:LEU164 4.9 30.9 1.0

Chlorine binding site 10 out of 12 in 4r69

Go back to Chlorine Binding Sites List in 4r69
Chlorine binding site 10 out of 12 in the Lactate Dehydrogenase in Complex with Inhibitor Compound 13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Lactate Dehydrogenase in Complex with Inhibitor Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl803

b:46.6
occ:1.00
 CL1 D:W13803 0.0 46.6 1.0
C2 D:W13803 1.7 41.7 1.0
C3 D:W13803 2.7 41.6 1.0
C15 D:W13803 2.8 37.3 1.0
C16 D:W13803 3.2 34.0 1.0
C17 D:W13803 3.5 31.9 1.0
C30 D:W13803 3.5 33.5 1.0
CB D:ARG98 3.7 48.1 1.0
CD D:ARG98 3.7 45.1 1.0
C6N D:NAI801 3.8 30.0 1.0
C2D D:NAI801 4.0 32.0 1.0
O2D D:NAI801 4.0 32.4 1.0
C4 D:W13803 4.0 41.0 1.0
C13 D:W13803 4.0 38.3 1.0
CD1 D:ILE241 4.1 44.6 1.0
OG1 D:THR247 4.2 56.1 1.0
CG D:ARG98 4.3 48.1 1.0
C5N D:NAI801 4.3 31.1 1.0
O1N D:NAI801 4.5 35.1 1.0
C5 D:W13803 4.6 40.1 1.0
N1N D:NAI801 4.7 30.3 1.0
C18 D:W13803 4.8 30.4 1.0
C28 D:W13803 4.8 33.5 1.0
O5D D:NAI801 4.8 34.1 1.0
C1D D:NAI801 4.9 30.6 1.0
N D:THR247 4.9 45.1 1.0
CA D:ARG98 5.0 50.5 1.0
NE D:ARG98 5.0 48.1 1.0

Reference:

S.Labadie, P.S.Dragovich, J.Chen, B.P.Fauber, J.Boggs, L.B.Corson, C.Z.Ding, C.Eigenbrot, H.Ge, Q.Ho, K.W.Lai, S.Ma, S.Malek, D.Peterson, H.E.Purkey, K.Robarge, L.Salphati, S.Sideris, M.Ultsch, E.Vanderporten, B.Wei, Q.Xu, I.Yen, Q.Yue, H.Zhang, X.Zhang, A.Zhou. Optimization of 5-(2,6-Dichlorophenyl)-3-Hydroxy-2-Mercaptocyclohex-2-Enones As Potent Inhibitors of Human Lactate Dehydrogenase. Bioorg.Med.Chem.Lett. V. 25 75 2014.
ISSN: ISSN 0960-894X
PubMed: 25466195
DOI: 10.1016/J.BMCL.2014.11.008
Page generated: Fri Jul 26 01:09:26 2024

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