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Chlorine 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:

Fluorine (F) 4 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 4 in 6bb3

Go back to Chlorine Binding Sites List in 6bb3
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl404

b:44.6
occ:1.00
 CL35 A:D4A404 0.0 44.6 1.0
C19 A:D4A404 1.7 41.9 1.0
C9 A:D4A404 2.7 40.0 1.0
C18 A:D4A404 2.7 38.8 1.0
NH2 A:ARG168 3.1 42.1 1.0
S34 A:D4A404 3.1 38.4 1.0
OD2 A:ASP165 3.5 43.0 1.0
CG A:ASP165 3.5 44.1 1.0
OD1 A:ASP165 3.8 46.7 1.0
CA A:ASP165 3.9 33.0 1.0
C2 A:D4A404 4.0 37.5 1.0
C8 A:D4A404 4.0 36.6 1.0
N A:ASP165 4.1 33.6 1.0
CB A:ASP165 4.1 34.6 1.0
NE2 A:HIS192 4.1 38.3 1.0
CD A:ARG168 4.2 31.7 1.0
CZ A:ARG168 4.3 57.5 1.0
CG1 A:VAL233 4.3 38.4 1.0
CD2 A:HIS192 4.5 38.1 1.0
C1 A:D4A404 4.5 36.9 1.0
CG A:LEU164 4.5 38.4 1.0
C A:LEU164 4.5 37.4 1.0
CD2 A:LEU164 4.7 39.1 1.0
NE A:ARG168 4.7 43.1 1.0
CB A:ALA237 4.7 31.4 1.0
C22 A:D4A404 4.7 37.2 1.0
O A:VAL233 4.8 39.1 1.0
O A:LEU164 4.8 37.1 1.0
CB A:LEU164 4.9 34.0 1.0
CA A:GLY193 5.0 34.1 1.0

Chlorine binding site 2 out of 4 in 6bb3

Go back to Chlorine Binding Sites List in 6bb3
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl404

b:41.9
occ:1.00
 CL35 B:D4A404 0.0 41.9 1.0
C19 B:D4A404 1.7 39.1 1.0
C9 B:D4A404 2.7 36.2 1.0
C18 B:D4A404 2.7 37.1 1.0
S34 B:D4A404 3.1 33.6 1.0
NH2 B:ARG168 3.1 30.4 1.0
CG B:ASP165 3.4 42.3 1.0
OD2 B:ASP165 3.5 47.3 1.0
OD1 B:ASP165 3.7 41.3 1.0
CA B:ASP165 3.7 29.8 1.0
N B:ASP165 3.9 29.6 1.0
C2 B:D4A404 4.0 35.6 1.0
C8 B:D4A404 4.0 35.4 1.0
CB B:ASP165 4.0 32.5 1.0
CE1 B:HIS192 4.1 37.6 1.0
CG1 B:VAL233 4.1 28.6 1.0
CD B:ARG168 4.2 39.4 1.0
CZ B:ARG168 4.3 49.2 1.0
C B:LEU164 4.4 34.7 1.0
CG B:LEU164 4.4 32.0 1.0
C1 B:D4A404 4.5 34.9 1.0
CD2 B:LEU164 4.6 31.4 1.0
ND1 B:HIS192 4.6 38.2 1.0
NE B:ARG168 4.7 46.6 1.0
O B:LEU164 4.7 36.7 1.0
C22 B:D4A404 4.7 35.1 1.0
CB B:ALA237 4.8 34.1 1.0
CB B:LEU164 4.8 28.8 1.0
O B:VAL233 4.9 33.4 1.0
O29 B:D4A404 5.0 35.4 1.0
NE2 B:HIS192 5.0 38.4 1.0

Chlorine binding site 3 out of 4 in 6bb3

Go back to Chlorine Binding Sites List in 6bb3
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl404

b:45.2
occ:1.00
 CL35 C:D4A404 0.0 45.2 1.0
C19 C:D4A404 1.7 37.6 1.0
C9 C:D4A404 2.7 36.7 1.0
C18 C:D4A404 2.7 35.7 1.0
NH2 C:ARG168 3.1 34.1 1.0
S34 C:D4A404 3.1 35.2 1.0
CG C:ASP165 3.5 46.1 1.0
OD2 C:ASP165 3.6 45.5 1.0
OD1 C:ASP165 3.8 48.0 1.0
CA C:ASP165 3.8 31.6 1.0
C2 C:D4A404 4.0 39.2 1.0
N C:ASP165 4.0 32.3 1.0
C8 C:D4A404 4.0 37.2 1.0
CB C:ASP165 4.1 33.2 1.0
CD C:ARG168 4.1 29.9 1.0
CG1 C:VAL233 4.1 33.2 1.0
CE1 C:HIS192 4.2 41.1 1.0
CZ C:ARG168 4.2 53.9 1.0
C C:LEU164 4.5 36.1 1.0
CG C:LEU164 4.5 37.2 1.0
C1 C:D4A404 4.5 39.2 1.0
NE C:ARG168 4.6 39.2 1.0
CB C:ALA237 4.6 36.9 1.0
CD2 C:LEU164 4.6 40.0 1.0
ND1 C:HIS192 4.7 41.7 1.0
C22 C:D4A404 4.8 37.1 1.0
O C:LEU164 4.8 36.6 1.0
CB C:LEU164 4.9 32.2 1.0

Chlorine binding site 4 out of 4 in 6bb3

Go back to Chlorine Binding Sites List in 6bb3
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl403

b:43.8
occ:1.00
 CL35 D:D4A403 0.0 43.8 1.0
C19 D:D4A403 1.7 40.7 1.0
C9 D:D4A403 2.7 40.4 1.0
C18 D:D4A403 2.7 36.2 1.0
NH2 D:ARG168 3.1 39.0 1.0
S34 D:D4A403 3.2 36.2 1.0
OD2 D:ASP165 3.5 44.6 1.0
CG D:ASP165 3.5 40.2 1.0
OD1 D:ASP165 3.8 41.9 1.0
CA D:ASP165 3.9 25.2 1.0
C2 D:D4A403 4.0 38.2 1.0
C8 D:D4A403 4.0 35.5 1.0
N D:ASP165 4.1 26.7 1.0
CB D:ASP165 4.1 26.7 1.0
CE1 D:HIS192 4.2 35.4 1.0
CD D:ARG168 4.2 32.2 1.0
CG1 D:VAL233 4.2 36.8 1.0
CZ D:ARG168 4.3 48.1 1.0
C1 D:D4A403 4.5 36.8 1.0
C D:LEU164 4.6 31.0 1.0
CG D:LEU164 4.6 35.1 1.0
CB D:ALA237 4.7 34.5 1.0
ND1 D:HIS192 4.7 36.3 1.0
NE D:ARG168 4.7 37.9 1.0
CD2 D:LEU164 4.7 35.9 1.0
O D:VAL233 4.8 36.9 1.0
C22 D:D4A403 4.8 36.2 1.0
O D:LEU164 4.9 30.3 1.0
CB D:LEU164 5.0 29.0 1.0
CA D:GLY193 5.0 31.3 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: Sat Jul 12 11:51:57 2025

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