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Fluorine 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:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 3 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6bb2

Go back to Fluorine Binding Sites List in 6bb2
Fluorine 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 Fluorine with other atoms in the F 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:F805

b:79.4
occ:1.00
 F1 D:D4J805 0.0 79.4 1.0
C2 D:D4J805 1.4 79.9 1.0
C3 D:D4J805 2.4 80.7 1.0
C5 D:D4J805 2.4 78.9 1.0
C4 D:D4J805 3.7 80.5 1.0
C6 D:D4J805 3.7 78.4 1.0
CE1 D:TYR238 3.8 40.8 1.0
OH D:TYR238 3.8 38.8 1.0
S30 D:D4J805 4.0 61.7 1.0
C7 D:D4J805 4.2 78.4 1.0
CZ D:TYR238 4.3 44.4 1.0
C29 D:D4J805 4.9 58.7 1.0
CD1 D:TYR238 4.9 39.3 1.0

Fluorine binding site 2 out of 3 in 6bb2

Go back to Fluorine Binding Sites List in 6bb2
Fluorine 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 Fluorine with other atoms in the F 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:F802

b:92.9
occ:1.00
 F1 E:D4J802 0.0 92.9 1.0
C2 E:D4J802 1.4 93.7 1.0
C3 E:D4J802 2.4 94.4 1.0
C5 E:D4J802 2.4 92.8 1.0
C6 E:D4J802 3.7 92.4 1.0
C4 E:D4J802 3.7 94.0 1.0
CE1 E:TYR238 4.0 45.4 1.0
C7 E:D4J802 4.2 92.4 1.0
OH E:TYR238 4.7 52.8 1.0
S30 E:D4J802 4.7 85.9 1.0
CZ E:TYR238 4.8 51.1 1.0
CD1 E:TYR238 4.8 45.3 1.0

Fluorine binding site 3 out of 3 in 6bb2

Go back to Fluorine Binding Sites List in 6bb2
Fluorine 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 Fluorine with other atoms in the F 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:F802

b:95.8
occ:1.00
 F1 G:D4J802 0.0 95.8 1.0
C2 G:D4J802 1.4 95.6 1.0
C3 G:D4J802 2.4 94.9 1.0
C5 G:D4J802 2.4 95.0 1.0
C6 G:D4J802 3.7 94.1 1.0
C4 G:D4J802 3.7 93.8 1.0
CE1 G:TYR238 4.0 45.6 1.0
C7 G:D4J802 4.2 92.2 1.0
S30 G:D4J802 4.5 66.9 1.0
O G:HOH963 4.7 43.8 1.0
CD1 G:TYR238 4.7 44.4 1.0
OH G:TYR238 4.9 53.1 1.0
CZ G:TYR238 4.9 52.1 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: Tue Jul 15 10:02:29 2025

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