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Fluorine in PDB 6baz: Lactate Dehydrogenase in Complex with Inhibitor (S)-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 (S)-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 (S)-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 (S)-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: 6baz 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) 46.30 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.700, 80.083, 103.673, 90.00, 97.37, 90.00
R / Rfree (%) 21.3 / 26.1

Other elements in 6baz:

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

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

Fluorine binding site 1 out of 2 in 6baz

Go back to Fluorine Binding Sites List in 6baz
Fluorine binding site 1 out of 2 in the Lactate Dehydrogenase in Complex with Inhibitor (S)-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 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-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:F403

b:0.2
occ:1.00
 F34 C:D47403 0.0 0.2 1.0
C31 C:D47403 1.4 0.3 1.0
C30 C:D47403 2.4 0.2 1.0
C32 C:D47403 2.4 0.1 1.0
CE2 C:TYR238 3.6 78.5 1.0
C29 C:D47403 3.6 0.8 1.0
C33 C:D47403 3.7 0.9 1.0
OH C:TYR238 4.1 87.3 1.0
C28 C:D47403 4.1 0.5 1.0
CZ C:TYR238 4.3 85.7 1.0
CD2 C:TYR238 4.5 77.2 1.0
C18 C:D47403 4.9 0.9 1.0

Fluorine binding site 2 out of 2 in 6baz

Go back to Fluorine Binding Sites List in 6baz
Fluorine binding site 2 out of 2 in the Lactate Dehydrogenase in Complex with Inhibitor (S)-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 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-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:F802

b:86.5
occ:1.00
 F34 D:D47802 0.0 86.5 1.0
C31 D:D47802 1.3 85.4 1.0
C30 D:D47802 2.4 85.1 1.0
C32 D:D47802 2.4 84.8 1.0
OE1 D:GLN99 3.5 95.0 1.0
C29 D:D47802 3.6 85.2 1.0
C33 D:D47802 3.6 85.0 1.0
CD D:GLN99 4.1 99.7 1.0
C28 D:D47802 4.1 85.4 1.0
OH D:TYR238 4.3 74.8 1.0
NE2 D:GLN99 4.3 90.7 1.0
CE1 D:TYR238 4.4 66.0 1.0
O D:GLU103 4.8 83.9 1.0
CZ D:TYR238 4.9 72.4 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: Thu Aug 1 18:03:05 2024

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