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Fluorine in PDB 6bad: Lactate Dehydrogenase in Complex with Inhibitor (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One

Enzymatic activity of Lactate Dehydrogenase in Complex with Inhibitor (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One

All present enzymatic activity of Lactate Dehydrogenase in Complex with Inhibitor (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One:
1.1.1.27;

Protein crystallography data

The structure of Lactate Dehydrogenase in Complex with Inhibitor (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One, PDB code: 6bad 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) 46.64 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.401, 80.714, 102.429, 90.00, 96.81, 90.00
R / Rfree (%) 19.4 / 23

Other elements in 6bad:

The structure of Lactate Dehydrogenase in Complex with Inhibitor (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Lactate Dehydrogenase in Complex with Inhibitor (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One (pdb code 6bad). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Lactate Dehydrogenase in Complex with Inhibitor (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One, PDB code: 6bad:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6bad

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Fluorine binding site 1 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-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 (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F805

b:27.4
occ:1.00
 F29 A:D0Y805 0.0 27.4 1.0
C28 A:D0Y805 1.4 25.4 1.0
C27 A:D0Y805 2.4 23.5 1.0
C30 A:D0Y805 2.4 22.2 1.0
O A:HOH1086 3.3 48.1 1.0
O8 A:EPE803 3.5 58.7 1.0
O A:HOH979 3.5 45.9 1.0
C5 A:EPE803 3.5 50.4 1.0
C26 A:D0Y805 3.6 23.7 1.0
C31 A:D0Y805 3.7 22.1 1.0
CE1 A:TYR238 4.0 26.0 1.0
N4 A:EPE803 4.0 51.9 1.0
C7 A:EPE803 4.0 55.0 1.0
C25 A:D0Y805 4.2 24.2 1.0
C6 A:EPE803 4.2 49.0 1.0
C8 A:EPE803 4.3 56.7 1.0
CD1 A:TYR238 4.6 25.8 1.0

Fluorine binding site 2 out of 4 in 6bad

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Fluorine binding site 2 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-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 (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F805

b:36.7
occ:1.00
 F29 B:D0Y805 0.0 36.7 1.0
C28 B:D0Y805 1.3 32.8 1.0
C27 B:D0Y805 2.4 28.1 1.0
C30 B:D0Y805 2.4 31.2 1.0
C7 B:EPE803 3.3 47.9 0.8
C3 B:EPE803 3.4 45.5 0.8
N4 B:EPE803 3.5 47.0 0.8
C26 B:D0Y805 3.6 26.5 1.0
C31 B:D0Y805 3.6 29.2 1.0
CE1 B:TYR238 3.9 14.8 1.0
C25 B:D0Y805 4.1 26.1 1.0
C2 B:EPE803 4.3 44.5 0.8
C8 B:EPE803 4.5 48.0 0.8
CD1 B:TYR238 4.5 17.8 1.0
O8 B:EPE803 4.5 48.9 0.8
C5 B:EPE803 5.0 45.5 0.8
CZ B:TYR238 5.0 17.6 1.0

Fluorine binding site 3 out of 4 in 6bad

Go back to Fluorine Binding Sites List in 6bad
Fluorine binding site 3 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-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 (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F807

b:26.6
occ:1.00
 F29 C:D0Y807 0.0 26.6 1.0
C28 C:D0Y807 1.4 26.6 1.0
C27 C:D0Y807 2.4 24.2 1.0
C30 C:D0Y807 2.4 23.1 1.0
O8 C:EPE803 2.8 52.5 0.9
C3 C:EPE803 3.2 38.5 0.9
O C:HOH991 3.2 33.8 1.0
C26 C:D0Y807 3.6 22.5 1.0
C31 C:D0Y807 3.7 22.7 1.0
C8 C:EPE803 3.7 51.5 0.9
O C:HOH923 3.8 37.1 1.0
C7 C:EPE803 4.1 47.9 0.9
CE1 C:TYR238 4.1 19.5 1.0
C25 C:D0Y807 4.2 21.4 1.0
N4 C:EPE803 4.2 42.9 0.9
C2 C:EPE803 4.3 34.6 0.9
CD1 C:TYR238 4.7 17.4 1.0

Fluorine binding site 4 out of 4 in 6bad

Go back to Fluorine Binding Sites List in 6bad
Fluorine binding site 4 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Lactate Dehydrogenase in Complex with Inhibitor (R)-3-((2- Chlorophenyl)Thio)-6-(3-((4-Fluorophenyl)Amino)Phenyl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F803

b:51.9
occ:1.00
 F29 D:D0Y803 0.0 51.9 1.0
C28 D:D0Y803 1.4 48.7 1.0
C27 D:D0Y803 2.4 44.5 1.0
C30 D:D0Y803 2.4 47.9 1.0
C26 D:D0Y803 3.6 41.0 1.0
C31 D:D0Y803 3.7 43.5 1.0
CE1 D:TYR238 3.9 18.9 1.0
OE1 D:GLN99 4.1 62.3 1.0
C25 D:D0Y803 4.2 38.4 1.0
CD1 D:TYR238 4.5 19.1 1.0
CD D:GLN99 4.7 61.7 1.0
NE2 D:GLN99 4.9 45.3 1.0
CZ D:TYR238 5.0 22.5 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: Thu Aug 1 18:02:24 2024

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