Chlorine in PDB 6bb2: Lactate Dehydrogenase in Complex with Inhibitor (S)-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 (S)-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 (S)-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 (S)-5-((2- Chlorophenyl)Thio)-6'-(4-Fluorophenoxy)-4-Hydroxy-2-(Thiophen-3-Yl)- 2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One, PDB code: 6bb2 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) 49.79 / 2.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.183, 158.561, 264.978, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.6

Other elements in 6bb2:

The structure of Lactate Dehydrogenase in Complex with Inhibitor (S)-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) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lactate Dehydrogenase in Complex with Inhibitor (S)-5-((2- Chlorophenyl)Thio)-6'-(4-Fluorophenoxy)-4-Hydroxy-2-(Thiophen-3-Yl)- 2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One (pdb code 6bb2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Lactate Dehydrogenase in Complex with Inhibitor (S)-5-((2- Chlorophenyl)Thio)-6'-(4-Fluorophenoxy)-4-Hydroxy-2-(Thiophen-3-Yl)- 2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One, PDB code: 6bb2:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6bb2

Go back to Chlorine Binding Sites List in 6bb2
Chlorine binding site 1 out of 3 in the Lactate Dehydrogenase in Complex with Inhibitor (S)-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 (S)-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:Cl805

b:43.6
occ:1.00
CL23 D:D4J805 0.0 43.6 1.0
C18 D:D4J805 1.7 45.0 1.0
C19 D:D4J805 2.7 46.1 1.0
C17 D:D4J805 2.8 46.1 1.0
OD2 D:ASP165 3.0 48.6 1.0
NH2 D:ARG168 3.0 57.2 1.0
CG D:ASP165 3.2 41.4 1.0
S16 D:D4J805 3.2 45.0 1.0
OD1 D:ASP165 3.7 44.2 1.0
CA D:ASP165 3.7 25.9 1.0
CE1 D:HIS192 3.8 35.3 1.0
CB D:ASP165 3.8 27.9 1.0
C20 D:D4J805 4.0 47.3 1.0
C22 D:D4J805 4.0 46.6 1.0
N D:ASP165 4.1 27.1 1.0
CD D:ARG168 4.2 34.1 1.0
CZ D:ARG168 4.2 60.0 1.0
ND1 D:HIS192 4.3 36.5 1.0
CG1 D:VAL233 4.3 45.5 1.0
O D:VAL233 4.4 44.3 1.0
C21 D:D4J805 4.5 46.5 1.0
CB D:ALA237 4.6 36.0 1.0
NE D:ARG168 4.7 42.1 1.0
C D:LEU164 4.7 34.7 1.0
NE2 D:HIS192 4.8 35.8 1.0
CG D:LEU164 4.8 39.7 1.0
C15 D:D4J805 5.0 46.1 1.0

Chlorine binding site 2 out of 3 in 6bb2

Go back to Chlorine Binding Sites List in 6bb2
Chlorine binding site 2 out of 3 in the Lactate Dehydrogenase in Complex with Inhibitor (S)-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 (S)-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:71.5
occ:1.00
CL23 E:D4J802 0.0 71.5 1.0
C18 E:D4J802 1.7 72.5 1.0
C19 E:D4J802 2.7 72.6 1.0
C17 E:D4J802 2.8 72.1 1.0
NH1 E:ARG168 3.0 45.2 1.0
S16 E:D4J802 3.3 70.1 1.0
CG E:ASP165 3.4 49.6 1.0
OD2 E:ASP165 3.5 55.3 1.0
OD1 E:ASP165 3.7 50.3 1.0
CA E:ASP165 3.7 33.9 1.0
CE1 E:HIS192 3.8 45.4 1.0
CB E:ASP165 3.9 35.8 1.0
N E:ASP165 4.0 34.0 1.0
C20 E:D4J802 4.0 72.8 1.0
C22 E:D4J802 4.1 72.4 1.0
CZ E:ARG168 4.2 61.2 1.0
ND1 E:HIS192 4.2 46.3 1.0
CD E:ARG168 4.2 49.3 1.0
O E:VAL233 4.3 54.3 1.0
CG1 E:VAL233 4.4 48.3 1.0
C21 E:D4J802 4.6 72.3 1.0
C E:LEU164 4.6 36.9 1.0
NE E:ARG168 4.7 49.1 1.0
CG E:LEU164 4.7 33.3 1.0
NE2 E:HIS192 4.8 45.4 1.0
O E:LEU164 4.9 37.5 1.0
CD2 E:LEU164 5.0 34.2 1.0
C E:ASP165 5.0 35.1 1.0

Chlorine binding site 3 out of 3 in 6bb2

Go back to Chlorine Binding Sites List in 6bb2
Chlorine binding site 3 out of 3 in the Lactate Dehydrogenase in Complex with Inhibitor (S)-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 (S)-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:Cl802

b:51.8
occ:1.00
CL23 G:D4J802 0.0 51.8 1.0
C18 G:D4J802 1.8 54.9 1.0
C19 G:D4J802 2.7 55.1 1.0
C17 G:D4J802 2.8 55.6 1.0
NH2 G:ARG168 3.0 39.2 1.0
S16 G:D4J802 3.2 53.3 1.0
CG G:ASP165 3.5 53.7 1.0
OD2 G:ASP165 3.6 57.4 1.0
OD1 G:ASP165 3.7 54.7 1.0
CE1 G:HIS192 3.7 45.5 1.0
CA G:ASP165 4.0 39.2 1.0
C20 G:D4J802 4.0 54.8 1.0
CB G:ASP165 4.1 41.8 1.0
C22 G:D4J802 4.1 54.7 1.0
ND1 G:HIS192 4.2 46.2 1.0
CD G:ARG168 4.2 43.2 1.0
CZ G:ARG168 4.2 50.2 1.0
N G:ASP165 4.2 39.3 1.0
O G:VAL233 4.5 55.7 1.0
CG1 G:VAL233 4.5 48.1 1.0
C21 G:D4J802 4.6 55.2 1.0
NE G:ARG168 4.7 42.1 1.0
NE2 G:HIS192 4.7 45.9 1.0
CG G:LEU164 4.8 39.9 1.0
C G:LEU164 4.8 41.4 1.0
CB G:ALA237 4.9 44.1 1.0
C15 G:D4J802 4.9 56.9 1.0
CD2 G:LEU164 5.0 42.5 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: Sat Dec 12 12:46:04 2020

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