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Fluorine in PDB 6bb3: Lactate Dehydrogenase in Complex with Inhibitor 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One

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

All present enzymatic activity of Lactate Dehydrogenase in Complex with Inhibitor 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-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 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One, PDB code: 6bb3 was solved by Z.Chen, C.Eigenbrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.58 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.700, 80.798, 103.047, 90.00, 96.77, 90.00
R / Rfree (%) 20.8 / 22.4

Other elements in 6bb3:

The structure of Lactate Dehydrogenase in Complex with Inhibitor 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-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 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One (pdb code 6bb3). 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 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-4-Hydroxy-6- (Thiophen-3-Yl)-5,6-Dihydro-2H-Pyran-2-One, PDB code: 6bb3:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6bb3

Go back to Fluorine Binding Sites List in 6bb3
Fluorine binding site 1 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-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 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-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:F404

b:44.5
occ:1.00
 F32 A:D4A404 0.0 44.5 1.0
C17 A:D4A404 1.3 41.5 1.0
C7 A:D4A404 2.3 37.9 1.0
C6 A:D4A404 2.4 40.0 1.0
CD2 A:LEU108 3.4 47.8 1.0
CB A:ASN137 3.4 29.1 1.0
O A:ASN137 3.4 38.6 1.0
C A:ASN137 3.4 38.2 1.0
N A:PRO138 3.6 35.1 1.0
C5 A:D4A404 3.6 35.9 1.0
C4 A:D4A404 3.6 36.6 1.0
CD A:PRO138 3.8 36.6 1.0
CG A:LEU108 4.0 45.3 1.0
CA A:ASN137 4.1 31.6 1.0
C16 A:D4A404 4.1 35.9 1.0
CD1 A:LEU108 4.1 45.2 1.0
CA A:PRO138 4.4 34.8 1.0
CG A:ASN137 4.5 39.0 1.0
CG A:PRO138 4.6 41.4 1.0
CB A:PRO138 4.6 36.9 1.0
CG A:GLN99 4.6 62.2 1.0
ND2 A:ASN112 4.7 39.8 1.0

Fluorine binding site 2 out of 4 in 6bb3

Go back to Fluorine Binding Sites List in 6bb3
Fluorine binding site 2 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-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 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-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:F404

b:58.7
occ:1.00
 F32 B:D4A404 0.0 58.7 1.0
C17 B:D4A404 1.3 53.8 1.0
C7 B:D4A404 2.3 50.8 1.0
C6 B:D4A404 2.4 48.2 1.0
O B:HOH515 3.0 52.8 1.0
OD1 B:ASN137 3.4 39.2 1.0
CA B:PRO138 3.4 36.9 1.0
CB B:PRO138 3.4 38.4 1.0
C5 B:D4A404 3.6 48.3 1.0
C4 B:D4A404 3.6 45.3 1.0
CG B:ASN137 3.9 44.6 1.0
C16 B:D4A404 4.1 45.5 1.0
CB B:ASN137 4.3 33.8 1.0
C B:PRO138 4.3 40.3 1.0
N B:PRO138 4.4 37.8 1.0
N B:VAL139 4.4 37.0 1.0
O B:HIS192 4.4 41.1 1.0
CD2 B:HIS192 4.5 38.7 1.0
CG B:PRO138 4.7 42.9 1.0
ND2 B:ASN137 4.8 33.1 1.0
CA B:ASN137 4.9 34.9 1.0

Fluorine binding site 3 out of 4 in 6bb3

Go back to Fluorine Binding Sites List in 6bb3
Fluorine binding site 3 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-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 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-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:F404

b:66.8
occ:1.00
 F32 C:D4A404 0.0 66.8 1.0
C17 C:D4A404 1.3 64.3 1.0
C6 C:D4A404 2.3 62.6 1.0
C7 C:D4A404 2.4 63.5 1.0
CB C:PRO138 3.3 37.4 1.0
CA C:PRO138 3.3 35.4 1.0
N C:PRO138 3.5 35.7 1.0
CB C:ASN137 3.6 30.1 1.0
C4 C:D4A404 3.6 61.8 1.0
C5 C:D4A404 3.6 61.9 1.0
CG C:ASN137 3.9 49.4 1.0
CG C:PRO138 4.0 42.2 1.0
CD C:PRO138 4.0 37.6 1.0
C C:ASN137 4.0 36.0 1.0
OD1 C:ASN137 4.0 42.3 1.0
C16 C:D4A404 4.1 59.8 1.0
O C:HOH516 4.1 33.6 1.0
CA C:ASN137 4.3 29.2 1.0
O C:ASN137 4.7 35.4 1.0
ND2 C:ASN137 4.7 38.3 1.0
C C:PRO138 4.8 37.0 1.0

Fluorine binding site 4 out of 4 in 6bb3

Go back to Fluorine Binding Sites List in 6bb3
Fluorine binding site 4 out of 4 in the Lactate Dehydrogenase in Complex with Inhibitor 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-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 3-((2-Chlorophenyl) Thio)-6-(6-((4-Fluorophenyl)Amino)Pyridin-2-Yl)-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:F403

b:61.7
occ:1.00
 F32 D:D4A403 0.0 61.7 1.0
C17 D:D4A403 1.3 61.2 1.0
C6 D:D4A403 2.3 59.3 1.0
C7 D:D4A403 2.4 60.5 1.0
O D:HOH533 3.2 39.5 1.0
CA D:PRO138 3.2 28.9 1.0
CB D:PRO138 3.3 30.1 1.0
CB D:ASN137 3.4 27.1 1.0
OD1 D:ASN137 3.4 25.8 1.0
CG D:ASN137 3.5 37.6 1.0
C4 D:D4A403 3.6 59.1 1.0
C5 D:D4A403 3.6 59.6 1.0
N D:PRO138 3.6 29.4 1.0
C16 D:D4A403 4.1 57.7 1.0
C D:ASN137 4.1 32.5 1.0
CA D:ASN137 4.2 29.2 1.0
CG D:PRO138 4.2 34.5 1.0
ND2 D:ASN137 4.3 32.0 1.0
CD D:PRO138 4.3 30.4 1.0
CD2 D:LEU108 4.4 51.1 1.0
C D:PRO138 4.5 32.0 1.0
N D:VAL139 4.7 28.0 1.0
O D:ASN137 5.0 32.1 1.0

Reference:

B.Q.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.Gao, 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 10:02:30 2025

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