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Chlorine in PDB 6bag: Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One

Enzymatic activity of Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One

All present enzymatic activity of Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One:
1.1.1.27;

Protein crystallography data

The structure of Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One, PDB code: 6bag was solved by M.Ultsch, C.Eigenbrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.07 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.799, 81.007, 102.756, 90.00, 98.53, 90.00
R / Rfree (%) 17.5 / 21.3

Other elements in 6bag:

The structure of Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One (pdb code 6bag). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One, PDB code: 6bag:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6bag

Go back to Chlorine Binding Sites List in 6bag
Chlorine binding site 1 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One


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 (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:34.7
occ:1.00
 CL8 A:D0V404 0.0 34.7 1.0
C7 A:D0V404 1.7 34.8 1.0
C9 A:D0V404 2.7 36.3 1.0
C6 A:D0V404 2.8 34.2 1.0
S5 A:D0V404 3.2 33.6 1.0
NH2 A:ARG168 3.3 36.0 1.0
CG A:ASP165 3.4 32.7 1.0
OD2 A:ASP165 3.5 28.5 1.0
CA A:ASP165 3.7 28.4 1.0
OD1 A:ASP165 3.8 31.5 1.0
O A:HOH513 3.8 29.1 1.0
CB A:ASP165 3.9 29.6 1.0
N A:ASP165 4.0 29.4 1.0
CG1 A:VAL233 4.0 33.1 1.0
C10 A:D0V404 4.0 34.9 1.0
C12 A:D0V404 4.1 31.9 1.0
CE1 A:HIS192 4.1 29.3 1.0
CD A:ARG168 4.2 30.7 1.0
CZ A:ARG168 4.4 46.3 1.0
CG A:LEU164 4.5 34.9 1.0
O A:VAL233 4.5 34.8 1.0
C11 A:D0V404 4.6 31.4 1.0
C A:LEU164 4.6 33.5 1.0
ND1 A:HIS192 4.6 30.1 1.0
CD2 A:LEU164 4.7 36.2 1.0
NE A:ARG168 4.8 36.0 1.0
CB A:ALA237 4.8 30.6 1.0
C4 A:D0V404 4.9 34.9 1.0
CB A:LEU164 4.9 30.3 1.0
O A:LEU164 4.9 33.0 1.0
CA A:GLY193 4.9 27.5 1.0
NE2 A:HIS192 4.9 29.4 1.0

Chlorine binding site 2 out of 4 in 6bag

Go back to Chlorine Binding Sites List in 6bag
Chlorine binding site 2 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One


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 (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:33.0
occ:1.00
 CL8 B:D0V404 0.0 33.0 1.0
C7 B:D0V404 1.8 32.6 1.0
C9 B:D0V404 2.7 33.6 1.0
C6 B:D0V404 2.8 32.5 1.0
S5 B:D0V404 3.2 34.3 1.0
NH2 B:ARG168 3.3 29.1 1.0
CG B:ASP165 3.4 29.2 1.0
OD2 B:ASP165 3.6 32.7 1.0
CA B:ASP165 3.7 24.5 1.0
OD1 B:ASP165 3.7 28.0 1.0
N B:ASP165 3.9 24.4 1.0
CB B:ASP165 3.9 25.1 1.0
CE1 B:HIS192 4.0 28.6 1.0
C10 B:D0V404 4.0 33.9 1.0
O B:HOH511 4.0 32.9 1.0
C12 B:D0V404 4.1 31.8 1.0
CG1 B:VAL233 4.1 31.6 1.0
CD B:ARG168 4.2 32.0 1.0
CG B:LEU164 4.4 27.5 1.0
CZ B:ARG168 4.5 38.4 1.0
C B:LEU164 4.5 26.6 1.0
C11 B:D0V404 4.6 33.4 1.0
ND1 B:HIS192 4.6 29.4 1.0
O B:VAL233 4.6 35.0 1.0
CD2 B:LEU164 4.7 29.8 1.0
O B:LEU164 4.7 23.7 1.0
NE B:ARG168 4.8 36.7 1.0
CB B:ALA237 4.8 31.6 1.0
C4 B:D0V404 4.8 37.0 1.0
CB B:LEU164 4.8 24.9 1.0
NE2 B:HIS192 4.9 28.8 1.0

Chlorine binding site 3 out of 4 in 6bag

Go back to Chlorine Binding Sites List in 6bag
Chlorine binding site 3 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One


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 (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:39.0
occ:1.00
 CL8 C:D0V404 0.0 39.0 1.0
C7 C:D0V404 1.7 36.2 1.0
C9 C:D0V404 2.7 37.1 1.0
C6 C:D0V404 2.7 34.6 1.0
S5 C:D0V404 3.2 34.6 1.0
NH2 C:ARG168 3.2 34.4 1.0
CG C:ASP165 3.5 29.0 1.0
OD2 C:ASP165 3.6 34.9 1.0
CA C:ASP165 3.7 24.1 1.0
OD1 C:ASP165 3.8 27.2 1.0
CB C:ASP165 3.9 25.0 1.0
N C:ASP165 3.9 25.7 1.0
CG1 C:VAL233 4.0 34.0 1.0
O C:HOH506 4.0 26.6 1.0
C10 C:D0V404 4.0 37.8 1.0
C12 C:D0V404 4.0 31.9 1.0
CD C:ARG168 4.2 35.9 1.0
CE1 C:HIS192 4.2 31.7 1.0
CZ C:ARG168 4.4 39.3 1.0
C C:LEU164 4.5 29.8 1.0
O C:VAL233 4.5 34.1 1.0
C11 C:D0V404 4.5 34.9 1.0
CG C:LEU164 4.6 30.9 1.0
ND1 C:HIS192 4.7 32.6 1.0
NE C:ARG168 4.7 28.7 1.0
CB C:ALA237 4.8 32.7 1.0
CD2 C:LEU164 4.8 32.1 1.0
C4 C:D0V404 4.9 33.5 1.0
O C:LEU164 4.9 30.0 1.0
CB C:LEU164 5.0 26.6 1.0
C C:ASP165 5.0 25.6 1.0

Chlorine binding site 4 out of 4 in 6bag

Go back to Chlorine Binding Sites List in 6bag
Chlorine binding site 4 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One


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 (R)-5-((2- Chlorophenyl)Thio)-6'-((4-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl803

b:34.5
occ:1.00
 CL8 D:D0V803 0.0 34.5 1.0
C7 D:D0V803 1.7 33.9 1.0
C6 D:D0V803 2.7 35.0 1.0
C9 D:D0V803 2.7 32.3 1.0
S5 D:D0V803 3.1 33.3 1.0
NH2 D:ARG168 3.3 28.9 1.0
CG D:ASP165 3.4 26.9 1.0
OD2 D:ASP165 3.5 27.5 1.0
CA D:ASP165 3.7 23.5 1.0
OD1 D:ASP165 3.7 23.4 1.0
N D:ASP165 3.9 24.1 1.0
CB D:ASP165 3.9 24.6 1.0
C12 D:D0V803 4.0 33.9 1.0
CE1 D:HIS192 4.0 26.8 1.0
C10 D:D0V803 4.0 31.7 1.0
O D:HOH906 4.1 27.6 1.0
CG1 D:VAL233 4.2 29.5 1.0
CD D:ARG168 4.2 23.1 1.0
CZ D:ARG168 4.4 36.1 1.0
C D:LEU164 4.4 28.2 1.0
CG D:LEU164 4.4 28.8 1.0
C11 D:D0V803 4.6 32.6 1.0
CD2 D:LEU164 4.6 26.4 1.0
ND1 D:HIS192 4.6 28.0 1.0
O D:VAL233 4.7 29.1 1.0
O D:LEU164 4.8 26.5 1.0
NE D:ARG168 4.8 20.1 1.0
CB D:LEU164 4.8 25.3 1.0
C4 D:D0V803 4.8 33.7 1.0
CB D:ALA237 4.8 28.9 1.0
NE2 D:HIS192 4.9 27.0 1.0
CA D:GLY193 5.0 28.8 1.0

Reference:

B.Wei, S.S.Labadie, K.Robarge, J.Chen, Z.Chen, L.B.Corson, C.Z.Ding, A.G.Dipasquale, P.S.Dragovich, C.Eigenbrot, M.Evangelista, B.P.Fauber, Z.Goa, H.Ge, A.Hitz, Q.Ho, K.W.Lai, W.Liu, Y.Liu, C.Li, S.Ma, S.Malek, T.O'brien, J.Pang, D.Peterson, L.Salphati, S.Sideris, M.Ultsch, I.Yen, Q.Yue, H.Zhang, A.Zhou, H.E.Purkey. Structure-Guided Optimization and in Vivo Activities of Hydroxylactone and Hydroxylactam Inhibitors of Human Lactate Dehydrogenase To Be Published.
Page generated: Fri Jul 26 22:39:49 2024

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