Atomistry » Chlorine » PDB 6b4f-6bb1 » 6bb1
Atomistry »
  Chlorine »
    PDB 6b4f-6bb1 »
      6bb1 »

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

Go back to Chlorine Binding Sites List in 6bb1
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

Go back to Chlorine Binding Sites List in 6bb1
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.
Page generated: Fri Jul 26 22:42:12 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy