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Chlorine in PDB 6bb0: 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: 6bb0 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) 38.65 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.125, 80.968, 103.214, 90.00, 98.33, 90.00
R / Rfree (%) 16.6 / 21.5

Chlorine Binding Sites:

The binding sites of Chlorine 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 6bb0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine 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: 6bb0:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6bb0

Go back to Chlorine Binding Sites List in 6bb0
Chlorine binding site 1 out of 3 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 Chlorine with other atoms in the Cl 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:Cl804

b:44.4
occ:1.00
 CL1 A:D3S804 0.0 44.4 1.0
C2 A:D3S804 1.8 50.6 1.0
C3 A:D3S804 2.7 59.0 1.0
NH2 A:ARG168 2.7 41.2 1.0
C7 A:D3S804 2.8 39.9 1.0
OD2 A:ASP165 3.2 30.2 1.0
CG A:ASP165 3.4 30.8 1.0
S8 A:D3S804 3.4 41.1 1.0
CA A:ASP165 3.8 29.9 1.0
OD1 A:ASP165 3.8 29.5 1.0
CB A:ASP165 3.9 30.9 1.0
CZ A:ARG168 3.9 38.3 1.0
CG1 A:VAL233 4.0 44.0 1.0
O A:HOH935 4.0 30.5 1.0
C4 A:D3S804 4.0 50.3 1.0
CD A:ARG168 4.1 36.0 1.0
O A:VAL233 4.1 43.4 1.0
CE1 A:HIS192 4.1 30.9 1.0
C6 A:D3S804 4.1 46.4 1.0
N A:ASP165 4.2 28.7 1.0
NE A:ARG168 4.4 37.0 1.0
C5 A:D3S804 4.6 41.9 1.0
ND1 A:HIS192 4.6 28.5 1.0
CB A:ALA237 4.7 42.0 1.0
CG A:LEU164 4.7 30.5 1.0
C A:LEU164 4.8 26.4 1.0
CD2 A:LEU164 4.8 36.0 1.0
C A:VAL233 4.9 46.6 1.0
O A:LEU164 5.0 24.3 1.0
CA A:GLY193 5.0 35.1 1.0
NE2 A:HIS192 5.0 30.9 1.0

Chlorine binding site 2 out of 3 in 6bb0

Go back to Chlorine Binding Sites List in 6bb0
Chlorine binding site 2 out of 3 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 Chlorine with other atoms in the Cl 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
C:Cl804

b:50.7
occ:1.00
 CL1 C:D3S804 0.0 50.7 1.0
C2 C:D3S804 1.8 46.5 1.0
C3 C:D3S804 2.7 41.7 1.0
C7 C:D3S804 2.8 34.1 1.0
NH2 C:ARG168 3.0 44.3 1.0
S8 C:D3S804 3.4 43.5 1.0
CG C:ASP165 3.4 34.4 1.0
OD2 C:ASP165 3.4 34.7 1.0
CA C:ASP165 3.6 21.9 1.0
OD1 C:ASP165 3.7 41.6 1.0
CB C:ASP165 3.9 28.6 1.0
N C:ASP165 3.9 26.0 1.0
CE1 C:HIS192 3.9 41.5 1.0
CG1 C:VAL233 4.0 37.2 1.0
C4 C:D3S804 4.0 48.6 1.0
C6 C:D3S804 4.1 48.9 1.0
CD C:ARG168 4.2 31.1 1.0
CZ C:ARG168 4.2 38.4 1.0
O C:VAL233 4.4 45.4 1.0
C C:LEU164 4.5 28.7 1.0
ND1 C:HIS192 4.5 31.7 1.0
C5 C:D3S804 4.6 48.9 1.0
CG C:LEU164 4.6 36.0 1.0
NE C:ARG168 4.6 32.1 1.0
CB C:ALA237 4.8 49.5 1.0
O C:LEU164 4.8 29.1 1.0
NE2 C:HIS192 4.9 37.3 1.0
C C:ASP165 4.9 34.1 1.0
CB C:LEU164 5.0 28.9 1.0

Chlorine binding site 3 out of 3 in 6bb0

Go back to Chlorine Binding Sites List in 6bb0
Chlorine binding site 3 out of 3 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 Chlorine with other atoms in the Cl 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
D:Cl802

b:40.5
occ:1.00
 CL1 D:D3S802 0.0 40.5 1.0
C2 D:D3S802 1.7 41.6 1.0
C3 D:D3S802 2.7 36.8 1.0
C7 D:D3S802 2.7 35.9 1.0
NH2 D:ARG168 3.1 33.5 1.0
S8 D:D3S802 3.3 33.6 1.0
CG D:ASP165 3.4 29.1 1.0
OD2 D:ASP165 3.4 26.1 1.0
CA D:ASP165 3.6 27.2 1.0
OD1 D:ASP165 3.7 26.4 1.0
N D:ASP165 3.8 22.4 1.0
CB D:ASP165 3.8 27.1 1.0
C4 D:D3S802 4.0 39.8 1.0
CD D:ARG168 4.0 25.4 1.0
C6 D:D3S802 4.0 41.4 1.0
CG1 D:VAL233 4.0 30.9 1.0
CE1 D:HIS192 4.1 37.7 1.0
O D:HOH918 4.1 27.6 1.0
CZ D:ARG168 4.2 37.0 1.0
C D:LEU164 4.4 32.2 1.0
C5 D:D3S802 4.5 34.2 1.0
O D:VAL233 4.5 36.2 1.0
CG D:LEU164 4.6 27.3 1.0
ND1 D:HIS192 4.6 24.8 1.0
NE D:ARG168 4.6 22.5 1.0
CB D:ALA237 4.7 40.1 1.0
O D:LEU164 4.8 23.4 1.0
CD2 D:LEU164 4.8 32.4 1.0
CB D:LEU164 4.8 27.2 1.0
C9 D:D3S802 4.9 39.7 1.0
C D:ASP165 4.9 27.5 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: Fri Jul 26 22:41:53 2024

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