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Chlorine in PDB 6bb1: Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-(4-Fluorophenoxy)-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-Fluorophenoxy)-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-Fluorophenoxy)-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-Fluorophenoxy)-4-Hydroxy-2-(Thiophen-3-Yl)- 2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One, PDB code: 6bb1 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) 48.74 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.605, 155.297, 265.615, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.8

Other elements in 6bb1:

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

Fluorine (F) 6 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-Fluorophenoxy)-4-Hydroxy-2-(Thiophen-3-Yl)- 2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One (pdb code 6bb1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-(4-Fluorophenoxy)-4-Hydroxy-2-(Thiophen-3-Yl)- 2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One, PDB code: 6bb1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6bb1

Go back to Chlorine Binding Sites List in 6bb1
Chlorine binding site 1 out of 6 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-(4-Fluorophenoxy)-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-Fluorophenoxy)-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:Cl803

b:37.0
occ:1.00
 CL23 A:D3J803 0.0 37.0 1.0
C18 A:D3J803 1.7 32.5 1.0
C19 A:D3J803 2.7 33.8 1.0
C17 A:D3J803 2.8 30.9 1.0
S16 A:D3J803 3.2 30.9 1.0
NH2 A:ARG168 3.2 24.7 1.0
CG A:ASP165 3.5 33.3 1.0
OD2 A:ASP165 3.6 37.1 1.0
OD1 A:ASP165 3.7 31.1 1.0
CA A:ASP165 3.8 26.7 1.0
CB A:ASP165 4.0 27.6 1.0
CG1 A:VAL233 4.0 34.0 1.0
N A:ASP165 4.0 27.9 1.0
C20 A:D3J803 4.0 33.6 1.0
C22 A:D3J803 4.0 31.7 1.0
CE1 A:HIS192 4.1 30.9 1.0
CD A:ARG168 4.2 29.3 1.0
CZ A:ARG168 4.4 41.2 1.0
C A:LEU164 4.5 31.5 1.0
C21 A:D3J803 4.6 32.1 1.0
ND1 A:HIS192 4.6 32.0 1.0
O A:VAL233 4.6 32.7 1.0
CG A:LEU164 4.7 35.1 1.0
CB A:ALA237 4.7 32.0 1.0
NE A:ARG168 4.8 28.4 1.0
O A:LEU164 4.8 30.9 1.0
C15 A:D3J803 4.9 34.5 1.0
CD2 A:LEU164 4.9 38.9 1.0
CB A:LEU164 5.0 28.5 1.0

Chlorine binding site 2 out of 6 in 6bb1

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Chlorine binding site 2 out of 6 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-(4-Fluorophenoxy)-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-Fluorophenoxy)-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:Cl803

b:33.7
occ:1.00
 CL23 B:D3J803 0.0 33.7 1.0
C18 B:D3J803 1.7 34.1 1.0
C17 B:D3J803 2.7 35.2 1.0
C19 B:D3J803 2.7 34.6 1.0
S16 B:D3J803 3.1 34.1 1.0
NH2 B:ARG168 3.1 37.0 1.0
CG B:ASP165 3.4 33.0 1.0
OD2 B:ASP165 3.5 36.2 1.0
OD1 B:ASP165 3.5 28.4 1.0
CA B:ASP165 3.7 26.8 1.0
N B:ASP165 3.8 28.4 1.0
CE1 B:HIS192 3.9 36.8 1.0
CB B:ASP165 3.9 28.0 1.0
C22 B:D3J803 4.0 34.0 1.0
C20 B:D3J803 4.0 34.7 1.0
CD B:ARG168 4.2 28.7 1.0
CG1 B:VAL233 4.2 42.2 1.0
CZ B:ARG168 4.3 44.9 1.0
C B:LEU164 4.4 32.1 1.0
ND1 B:HIS192 4.4 37.6 1.0
CG B:LEU164 4.5 33.9 1.0
C21 B:D3J803 4.5 36.2 1.0
O B:LEU164 4.7 30.2 1.0
CD2 B:LEU164 4.7 34.2 1.0
NE B:ARG168 4.7 30.3 1.0
CB B:LEU164 4.7 29.7 1.0
C15 B:D3J803 4.8 34.3 1.0
CB B:ALA237 4.8 40.0 1.0
NE2 B:HIS192 4.9 37.1 1.0
O B:VAL233 4.9 40.6 1.0

Chlorine binding site 3 out of 6 in 6bb1

Go back to Chlorine Binding Sites List in 6bb1
Chlorine binding site 3 out of 6 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-(4-Fluorophenoxy)-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-Fluorophenoxy)-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:Cl804

b:40.6
occ:1.00
 CL23 D:D3J804 0.0 40.6 1.0
C18 D:D3J804 1.8 38.7 1.0
C17 D:D3J804 2.7 36.4 1.0
C19 D:D3J804 2.8 37.2 1.0
S16 D:D3J804 3.1 33.4 1.0
NH2 D:ARG168 3.2 27.5 1.0
CG D:ASP165 3.5 31.7 1.0
OD2 D:ASP165 3.6 33.1 1.0
OD1 D:ASP165 3.7 31.1 1.0
CA D:ASP165 3.8 23.9 1.0
O D:HOH916 3.8 35.1 1.0
N D:ASP165 4.0 24.4 1.0
C22 D:D3J804 4.1 36.2 1.0
CE1 D:HIS192 4.1 33.0 1.0
C20 D:D3J804 4.1 34.8 1.0
CB D:ASP165 4.1 25.0 1.0
CG1 D:VAL233 4.1 38.4 1.0
CD D:ARG168 4.2 31.1 1.0
CZ D:ARG168 4.3 38.7 1.0
C D:LEU164 4.5 28.4 1.0
ND1 D:HIS192 4.6 34.2 1.0
C21 D:D3J804 4.6 35.9 1.0
CG D:LEU164 4.6 31.1 1.0
O D:VAL233 4.7 37.9 1.0
CB D:ALA237 4.7 39.3 1.0
NE D:ARG168 4.7 31.4 1.0
C15 D:D3J804 4.8 37.0 1.0
O D:LEU164 4.8 29.5 1.0
CD2 D:LEU164 4.8 30.6 1.0
CB D:LEU164 4.9 26.6 1.0

Chlorine binding site 4 out of 6 in 6bb1

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Chlorine binding site 4 out of 6 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-(4-Fluorophenoxy)-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-Fluorophenoxy)-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
E:Cl802

b:55.2
occ:1.00
 CL23 E:D3J802 0.0 55.2 1.0
C18 E:D3J802 1.7 49.8 1.0
C19 E:D3J802 2.7 50.4 1.0
C17 E:D3J802 2.7 46.3 1.0
S16 E:D3J802 3.2 43.9 1.0
CG E:ASP165 3.5 44.4 1.0
NH1 E:ARG168 3.6 27.5 1.0
OD2 E:ASP165 3.6 44.7 1.0
OD1 E:ASP165 3.7 43.7 1.0
CA E:ASP165 3.7 34.1 1.0
N E:ASP165 4.0 34.3 1.0
CE1 E:HIS192 4.0 37.2 1.0
C20 E:D3J802 4.0 49.8 1.0
CB E:ASP165 4.0 36.0 1.0
C22 E:D3J802 4.0 45.9 1.0
CG1 E:VAL233 4.2 53.2 1.0
CD E:ARG168 4.2 36.9 1.0
C E:LEU164 4.5 36.5 1.0
ND1 E:HIS192 4.5 38.6 1.0
C21 E:D3J802 4.5 46.3 1.0
CG E:LEU164 4.6 38.8 1.0
CZ E:ARG168 4.7 40.8 1.0
O E:LEU164 4.7 34.7 1.0
CD2 E:LEU164 4.8 41.3 1.0
CB E:ALA237 4.8 39.1 1.0
O E:VAL233 4.9 51.0 1.0
C15 E:D3J802 4.9 44.9 1.0
CB E:LEU164 4.9 33.9 1.0
NE E:ARG168 4.9 38.7 1.0
NE2 E:HIS192 4.9 37.6 1.0

Chlorine binding site 5 out of 6 in 6bb1

Go back to Chlorine Binding Sites List in 6bb1
Chlorine binding site 5 out of 6 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-(4-Fluorophenoxy)-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 5 of Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-(4-Fluorophenoxy)-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
F:Cl803

b:53.7
occ:1.00
 CL23 F:D3J803 0.0 53.7 1.0
C18 F:D3J803 1.8 49.4 1.0
C19 F:D3J803 2.7 47.5 1.0
C17 F:D3J803 2.7 44.4 1.0
S16 F:D3J803 3.2 41.7 1.0
NH2 F:ARG168 3.3 29.0 1.0
CG F:ASP165 3.5 39.2 1.0
OD2 F:ASP165 3.5 38.2 1.0
OD1 F:ASP165 3.7 37.8 1.0
CA F:ASP165 3.8 31.7 1.0
CG1 F:VAL233 3.9 45.6 1.0
CB F:ASP165 4.0 33.6 1.0
C20 F:D3J803 4.0 45.0 1.0
C22 F:D3J803 4.1 43.5 1.0
N F:ASP165 4.1 32.6 1.0
CE1 F:HIS192 4.2 46.2 1.0
CD F:ARG168 4.3 34.7 1.0
O F:VAL233 4.4 43.6 1.0
CZ F:ARG168 4.5 47.7 1.0
C21 F:D3J803 4.6 42.9 1.0
CB F:ALA237 4.6 39.8 1.0
ND1 F:HIS192 4.6 46.8 1.0
C F:LEU164 4.7 37.8 1.0
C15 F:D3J803 4.9 44.6 1.0
CG F:LEU164 4.9 43.2 1.0
NE F:ARG168 4.9 32.4 1.0
C F:VAL233 4.9 44.7 1.0
CA F:GLY193 5.0 45.0 1.0
O F:LEU164 5.0 37.4 1.0

Chlorine binding site 6 out of 6 in 6bb1

Go back to Chlorine Binding Sites List in 6bb1
Chlorine binding site 6 out of 6 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-(4-Fluorophenoxy)-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 6 of Lactate Dehydrogenase in Complex with Inhibitor (R)-5-((2- Chlorophenyl)Thio)-6'-(4-Fluorophenoxy)-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
G:Cl803

b:46.2
occ:1.00
 CL23 G:D3J803 0.0 46.2 1.0
C18 G:D3J803 1.8 44.9 1.0
C17 G:D3J803 2.7 43.0 1.0
C19 G:D3J803 2.7 44.7 1.0
NH2 G:ARG168 3.0 39.3 1.0
S16 G:D3J803 3.1 40.5 1.0
CG G:ASP165 3.6 42.8 1.0
OD2 G:ASP165 3.6 47.2 1.0
OD1 G:ASP165 3.9 45.0 1.0
CA G:ASP165 3.9 29.2 1.0
C20 G:D3J803 4.0 45.0 1.0
C22 G:D3J803 4.0 42.2 1.0
N G:ASP165 4.1 29.8 1.0
CD G:ARG168 4.1 38.3 1.0
CB G:ASP165 4.1 31.4 1.0
CG1 G:VAL233 4.1 52.7 1.0
CE1 G:HIS192 4.1 37.1 1.0
CZ G:ARG168 4.2 46.8 1.0
C21 G:D3J803 4.6 44.4 1.0
C G:LEU164 4.6 37.0 1.0
CB G:ALA237 4.6 47.0 1.0
O G:VAL233 4.6 50.2 1.0
CG G:LEU164 4.6 37.3 1.0
NE G:ARG168 4.6 36.1 1.0
ND1 G:HIS192 4.7 38.0 1.0
CD2 G:LEU164 4.8 37.2 1.0
C15 G:D3J803 4.8 44.9 1.0
O G:LEU164 4.8 39.1 1.0
CB G:LEU164 4.9 33.8 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.
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