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Fluorine 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:

Chlorine (Cl) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 6 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6bb1

Go back to Fluorine Binding Sites List in 6bb1
Fluorine 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 Fluorine with other atoms in the F 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:F803

b:61.5
occ:1.00
 F1 A:D3J803 0.0 61.5 1.0
C2 A:D3J803 1.4 60.1 1.0
C5 A:D3J803 2.4 58.5 1.0
C3 A:D3J803 2.4 57.2 1.0
OD1 A:ASN137 3.4 27.6 1.0
O A:HIS192 3.6 31.2 1.0
CA A:PRO138 3.6 31.5 1.0
C6 A:D3J803 3.7 56.5 1.0
C4 A:D3J803 3.7 54.5 1.0
CB A:PRO138 3.8 33.5 1.0
CD2 A:HIS192 4.0 31.3 1.0
CG A:ASN137 4.0 35.9 1.0
C7 A:D3J803 4.2 52.7 1.0
N A:VAL139 4.3 30.8 1.0
C A:PRO138 4.4 34.6 1.0
CB A:ASN137 4.6 27.0 1.0
C A:HIS192 4.6 31.7 1.0
N A:PRO138 4.7 32.3 1.0
ND2 A:ASN137 4.8 23.4 1.0
CG A:HIS192 4.8 30.5 1.0
NE2 A:HIS192 4.9 30.8 1.0
CG A:PRO138 4.9 37.9 1.0
CB A:HIS192 5.0 27.5 1.0

Fluorine binding site 2 out of 6 in 6bb1

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Fluorine 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 Fluorine with other atoms in the F 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:F803

b:55.9
occ:1.00
 F1 B:D3J803 0.0 55.9 1.0
C2 B:D3J803 1.3 54.0 1.0
C3 B:D3J803 2.3 54.8 1.0
C5 B:D3J803 2.4 53.6 1.0
N B:PRO138 3.3 33.3 1.0
CB B:ASN137 3.3 27.1 1.0
CD2 B:LEU108 3.4 66.2 1.0
C B:ASN137 3.5 35.6 1.0
CG B:PRO138 3.6 40.0 1.0
C4 B:D3J803 3.6 53.8 1.0
CD B:PRO138 3.6 35.8 1.0
C6 B:D3J803 3.6 54.2 1.0
O B:ASN137 3.8 35.6 1.0
CA B:PRO138 3.8 32.6 1.0
CB B:PRO138 4.0 34.6 1.0
CA B:ASN137 4.0 29.3 1.0
C7 B:D3J803 4.1 51.0 1.0
CG B:ASN137 4.2 40.7 1.0
CG B:LEU108 4.7 63.6 1.0
OD1 B:ASN137 4.8 36.9 1.0
ND2 B:ASN137 4.8 36.9 1.0
CB B:LEU108 5.0 58.3 1.0

Fluorine binding site 3 out of 6 in 6bb1

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Fluorine 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 Fluorine with other atoms in the F 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:F804

b:63.6
occ:1.00
 F1 D:D3J804 0.0 63.6 1.0
C2 D:D3J804 1.4 58.7 1.0
C3 D:D3J804 2.4 55.8 1.0
C5 D:D3J804 2.4 55.4 1.0
CD2 D:LEU108 3.3 50.9 1.0
CB D:ASN137 3.5 27.4 1.0
C4 D:D3J804 3.6 53.3 1.0
C6 D:D3J804 3.6 53.4 1.0
N D:PRO138 3.8 30.6 1.0
C D:ASN137 3.8 31.4 1.0
CG D:PRO138 4.0 36.9 1.0
CD D:PRO138 4.0 32.3 1.0
O D:ASN137 4.0 30.0 1.0
C7 D:D3J804 4.1 50.6 1.0
CA D:PRO138 4.3 30.4 1.0
CA D:ASN137 4.4 26.0 1.0
CG D:LEU108 4.5 45.8 1.0
CB D:PRO138 4.5 32.5 1.0
CG D:ASN137 4.5 37.2 1.0
OE1 D:GLN99 4.8 69.8 1.0
CG D:ARG105 4.9 64.8 1.0
CD D:ARG105 5.0 67.5 1.0
CB D:LEU108 5.0 40.2 1.0

Fluorine binding site 4 out of 6 in 6bb1

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Fluorine 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 Fluorine with other atoms in the F 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:F802

b:72.3
occ:1.00
 F1 E:D3J802 0.0 72.3 1.0
C2 E:D3J802 1.4 71.8 1.0
C5 E:D3J802 2.4 72.4 1.0
C3 E:D3J802 2.4 69.2 1.0
O E:HOH945 2.7 29.6 1.0
CB E:PRO138 3.3 36.0 1.0
CA E:PRO138 3.3 34.7 1.0
C6 E:D3J802 3.6 71.3 1.0
C4 E:D3J802 3.6 68.9 1.0
OD1 E:ASN137 3.9 40.5 1.0
O E:HOH920 3.9 36.1 1.0
CG E:PRO138 3.9 40.2 1.0
N E:PRO138 4.0 34.7 1.0
O E:HOH963 4.0 44.6 1.0
CG E:ASN137 4.0 45.0 1.0
CB E:ASN137 4.1 33.5 1.0
C7 E:D3J802 4.1 68.7 1.0
O E:HOH935 4.3 29.6 1.0
C E:PRO138 4.6 40.8 1.0
CD E:PRO138 4.6 35.6 1.0
C E:ASN137 4.7 37.2 1.0
CA E:ASN137 4.8 30.4 1.0
ND2 E:ASN137 4.8 33.4 1.0
N E:VAL139 4.8 38.3 1.0
O E:HIS192 5.0 40.5 1.0

Fluorine binding site 5 out of 6 in 6bb1

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Fluorine 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 Fluorine with other atoms in the F 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:F803

b:86.2
occ:1.00
 F1 F:D3J803 0.0 86.2 1.0
C2 F:D3J803 1.4 84.7 1.0
C5 F:D3J803 2.4 83.5 1.0
C3 F:D3J803 2.4 82.2 1.0
CA F:PRO138 3.2 34.4 1.0
CB F:PRO138 3.3 35.9 1.0
OD1 F:ASN137 3.4 35.4 1.0
C6 F:D3J803 3.6 81.6 1.0
C4 F:D3J803 3.7 80.9 1.0
CG F:ASN137 3.8 51.1 1.0
CB F:ASN137 4.1 35.9 1.0
C7 F:D3J803 4.1 79.4 1.0
N F:PRO138 4.2 34.0 1.0
C F:PRO138 4.2 40.9 1.0
N F:VAL139 4.2 39.0 1.0
CG F:PRO138 4.3 40.1 1.0
O F:HIS192 4.4 47.8 1.0
O F:HOH939 4.5 42.7 1.0
CD2 F:HIS192 4.6 47.3 1.0
ND2 F:ASN137 4.6 41.4 1.0
CA F:ASN137 4.7 34.3 1.0
C F:ASN137 4.9 37.6 1.0
CD F:PRO138 5.0 36.0 1.0

Fluorine binding site 6 out of 6 in 6bb1

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Fluorine 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 Fluorine with other atoms in the F 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:F803

b:62.1
occ:1.00
 F1 G:D3J803 0.0 62.1 1.0
C2 G:D3J803 1.4 63.0 1.0
C3 G:D3J803 2.4 63.7 1.0
C5 G:D3J803 2.4 63.4 1.0
CB G:ASN137 3.4 28.6 1.0
N G:PRO138 3.4 35.5 1.0
C G:ASN137 3.5 38.0 1.0
C4 G:D3J803 3.6 63.2 1.0
C6 G:D3J803 3.6 63.1 1.0
CG G:PRO138 3.7 40.9 1.0
O G:ASN137 3.7 37.9 1.0
CD G:PRO138 3.7 36.5 1.0
CA G:PRO138 4.0 35.1 1.0
CA G:ASN137 4.1 31.1 1.0
C7 G:D3J803 4.1 60.7 1.0
CB G:PRO138 4.2 36.9 1.0
CG G:ARG105 4.4 72.4 1.0
CD2 G:LEU108 4.4 51.2 1.0
CG G:ASN137 4.4 41.8 1.0
CD G:ARG105 4.5 78.7 1.0
CG G:LEU108 5.0 48.4 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.
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