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Fluorine in PDB 6bag: Lactate Dehydrogenase in Complex with Inhibitor (R)-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 (R)-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 (R)-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 (R)-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: 6bag 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) 47.07 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.799, 81.007, 102.756, 90.00, 98.53, 90.00
R / Rfree (%) 17.5 / 21.3

Other elements in 6bag:

The structure of Lactate Dehydrogenase in Complex with Inhibitor (R)-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) 4 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-Fluorophenyl)Amino)-4-Hydroxy-2-(Thiophen- 3-Yl)-2,3-Dihydro-[2,2'-Bipyridin]-6(1H)-One (pdb code 6bag). 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)-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: 6bag:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6bag

Go back to Fluorine Binding Sites List in 6bag
Fluorine binding site 1 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-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 (R)-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
A:F404

b:42.8
occ:1.00
 F29 A:D0V404 0.0 42.8 1.0
C28 A:D0V404 1.3 39.1 1.0
C27 A:D0V404 2.4 39.4 1.0
C30 A:D0V404 2.4 37.3 1.0
CD2 A:LEU108 3.5 59.9 1.0
N A:PRO138 3.5 30.7 1.0
C A:ASN137 3.6 33.6 1.0
CB A:ASN137 3.6 29.5 1.0
C26 A:D0V404 3.6 40.3 1.0
C31 A:D0V404 3.6 38.7 1.0
CD A:PRO138 3.7 32.4 1.0
O A:ASN137 3.7 31.1 1.0
CG A:PRO138 3.7 36.5 1.0
C25 A:D0V404 4.1 41.7 1.0
CA A:PRO138 4.2 30.3 1.0
CA A:ASN137 4.2 30.5 1.0
CG A:LEU108 4.2 55.9 1.0
CB A:PRO138 4.4 32.0 1.0
CG A:ASN137 4.7 38.0 1.0

Fluorine binding site 2 out of 4 in 6bag

Go back to Fluorine Binding Sites List in 6bag
Fluorine binding site 2 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-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 (R)-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
B:F404

b:59.6
occ:1.00
 F29 B:D0V404 0.0 59.6 1.0
C28 B:D0V404 1.4 56.1 1.0
C30 B:D0V404 2.4 54.2 1.0
C27 B:D0V404 2.4 52.7 1.0
O B:ASN137 3.5 37.0 1.0
C B:ASN137 3.5 36.2 1.0
N B:PRO138 3.5 31.5 1.0
CD B:PRO138 3.6 32.8 1.0
C26 B:D0V404 3.6 51.2 1.0
C31 B:D0V404 3.7 52.1 1.0
CB B:ASN137 3.7 29.0 1.0
CG B:PRO138 3.8 36.1 1.0
CD2 B:LEU108 3.8 54.6 1.0
C25 B:D0V404 4.2 50.4 1.0
CA B:ASN137 4.3 30.3 1.0
CA B:PRO138 4.3 29.6 1.0
CB B:PRO138 4.5 30.9 1.0
CG B:LEU108 4.7 51.2 1.0
CG B:ASN137 4.8 37.6 1.0
ND2 B:ASN112 4.9 44.2 1.0
O B:HOH584 4.9 42.0 1.0

Fluorine binding site 3 out of 4 in 6bag

Go back to Fluorine Binding Sites List in 6bag
Fluorine binding site 3 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-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 3 of Lactate Dehydrogenase in Complex with Inhibitor (R)-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:F404

b:53.1
occ:1.00
 F29 C:D0V404 0.0 53.1 1.0
C28 C:D0V404 1.4 50.2 1.0
C30 C:D0V404 2.4 49.4 1.0
C27 C:D0V404 2.4 48.5 1.0
N C:PRO138 3.4 33.6 1.0
CG C:PRO138 3.5 39.3 1.0
CD C:PRO138 3.6 35.0 1.0
C C:ASN137 3.6 35.9 1.0
CB C:ASN137 3.6 26.8 1.0
C31 C:D0V404 3.6 48.6 1.0
C26 C:D0V404 3.7 47.1 1.0
O C:ASN137 3.8 35.5 1.0
CA C:PRO138 4.0 33.0 1.0
CB C:PRO138 4.1 34.9 1.0
C25 C:D0V404 4.1 45.7 1.0
CA C:ASN137 4.2 29.4 1.0
CD2 C:LEU108 4.4 61.8 1.0
CG C:ASN137 4.6 42.6 1.0

Fluorine binding site 4 out of 4 in 6bag

Go back to Fluorine Binding Sites List in 6bag
Fluorine binding site 4 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor (R)-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 4 of Lactate Dehydrogenase in Complex with Inhibitor (R)-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:F803

b:58.1
occ:1.00
 F29 D:D0V803 0.0 58.1 1.0
C28 D:D0V803 1.4 55.2 1.0
C27 D:D0V803 2.4 53.8 1.0
C30 D:D0V803 2.4 53.2 1.0
CD2 D:LEU108 3.3 54.6 1.0
O D:ASN137 3.5 29.3 1.0
C D:ASN137 3.5 30.4 1.0
CB D:ASN137 3.5 26.6 1.0
N D:PRO138 3.6 29.2 1.0
C26 D:D0V803 3.6 53.2 1.0
C31 D:D0V803 3.7 51.5 1.0
CD D:PRO138 3.7 30.8 1.0
CG D:LEU108 3.7 52.4 1.0
CG D:PRO138 3.9 35.0 1.0
CA D:ASN137 4.1 27.5 1.0
C25 D:D0V803 4.2 50.2 1.0
O D:HOH1008 4.3 47.0 1.0
CA D:PRO138 4.4 29.3 1.0
CB D:LEU108 4.5 46.9 1.0
CB D:PRO138 4.6 30.8 1.0
CG D:ASN137 4.6 33.5 1.0
CD1 D:LEU108 5.0 52.7 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 18:03:00 2024

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