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Chlorine in PDB 5ixs: Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-One

Enzymatic activity of Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-One

All present enzymatic activity of Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-One:
1.1.1.27;

Protein crystallography data

The structure of Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-One, PDB code: 5ixs 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) 37.80 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.624, 81.229, 104.797, 90.00, 97.56, 90.00
R / Rfree (%) 17.4 / 22.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-One (pdb code 5ixs). 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 Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-One, PDB code: 5ixs:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5ixs

Go back to Chlorine Binding Sites List in 5ixs
Chlorine binding site 1 out of 4 in the Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-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 Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:35.4
occ:1.00
 CL A:6EY403 0.0 35.4 1.0
C11 A:6EY403 1.7 43.7 1.0
C10 A:6EY403 2.7 47.4 1.0
C6 A:6EY403 2.7 31.2 1.0
NH2 A:ARG168 3.1 30.0 1.0
S5 A:6EY403 3.2 30.7 1.0
OD2 A:ASP165 3.3 26.4 1.0
CG A:ASP165 3.4 29.6 1.0
CA A:ASP165 3.7 24.9 1.0
OD1 A:ASP165 3.8 31.5 1.0
CB A:ASP165 3.9 33.2 1.0
N A:ASP165 3.9 27.3 1.0
CE1 A:HIS192 4.0 27.3 1.0
C9 A:6EY403 4.0 46.5 1.0
C7 A:6EY403 4.0 31.1 1.0
CD A:ARG168 4.1 27.1 1.0
CG1 A:VAL233 4.2 33.1 1.0
CZ A:ARG168 4.2 28.9 1.0
O A:HOH511 4.3 27.7 1.0
CG A:LEU164 4.4 24.0 1.0
C A:LEU164 4.4 27.5 1.0
C8 A:6EY403 4.5 32.5 1.0
ND1 A:HIS192 4.6 27.4 1.0
NE A:ARG168 4.6 25.4 1.0
CD2 A:LEU164 4.6 25.0 1.0
O A:VAL233 4.7 28.1 1.0
O A:LEU164 4.7 25.7 1.0
CB A:ALA237 4.7 38.6 1.0
C4 A:6EY403 4.9 26.5 1.0
CB A:LEU164 4.9 25.0 1.0
NE2 A:HIS192 4.9 26.4 1.0
C A:ASP165 5.0 24.0 1.0

Chlorine binding site 2 out of 4 in 5ixs

Go back to Chlorine Binding Sites List in 5ixs
Chlorine binding site 2 out of 4 in the Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-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 Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:41.9
occ:1.00
 CL B:6EY403 0.0 41.9 1.0
C11 B:6EY403 1.7 39.4 1.0
C10 B:6EY403 2.7 51.1 1.0
C6 B:6EY403 2.7 43.3 1.0
S5 B:6EY403 3.2 34.7 1.0
NH2 B:ARG168 3.3 32.6 1.0
CG B:ASP165 3.4 25.8 1.0
OD2 B:ASP165 3.5 28.0 1.0
CA B:ASP165 3.6 18.2 1.0
OD1 B:ASP165 3.7 36.0 1.0
CB B:ASP165 3.8 20.0 1.0
CG1 B:VAL233 3.9 29.5 1.0
CE1 B:HIS192 3.9 28.0 1.0
N B:ASP165 3.9 20.7 1.0
C9 B:6EY403 4.0 57.7 1.0
C7 B:6EY403 4.0 45.1 1.0
O B:HOH567 4.1 32.1 1.0
CD B:ARG168 4.3 28.1 1.0
O B:VAL233 4.4 41.8 1.0
CZ B:ARG168 4.5 31.0 1.0
ND1 B:HIS192 4.5 33.0 1.0
C8 B:6EY403 4.5 37.8 1.0
C B:LEU164 4.5 24.5 1.0
CG B:LEU164 4.6 27.6 1.0
CB B:ALA237 4.8 38.8 1.0
NE2 B:HIS192 4.8 31.3 1.0
O B:LEU164 4.9 24.5 1.0
NE B:ARG168 4.9 30.6 1.0
C4 B:6EY403 4.9 47.6 1.0
CD2 B:LEU164 4.9 34.2 1.0
C B:ASP165 5.0 18.1 1.0

Chlorine binding site 3 out of 4 in 5ixs

Go back to Chlorine Binding Sites List in 5ixs
Chlorine binding site 3 out of 4 in the Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-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 Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:43.5
occ:1.00
 CL C:6EY403 0.0 43.5 1.0
C11 C:6EY403 1.7 47.7 1.0
C10 C:6EY403 2.7 50.8 1.0
C6 C:6EY403 2.8 26.5 1.0
NH2 C:ARG168 3.2 49.3 1.0
S5 C:6EY403 3.3 45.7 1.0
CG C:ASP165 3.3 35.2 1.0
OD2 C:ASP165 3.4 41.2 1.0
OD1 C:ASP165 3.5 42.4 1.0
CA C:ASP165 3.6 28.5 1.0
CB C:ASP165 3.9 35.7 1.0
N C:ASP165 3.9 27.8 1.0
CG1 C:VAL233 4.0 42.9 1.0
CE1 C:HIS192 4.0 44.9 1.0
C9 C:6EY403 4.0 53.2 1.0
C7 C:6EY403 4.0 46.0 1.0
CD C:ARG168 4.2 40.4 1.0
CZ C:ARG168 4.3 44.1 1.0
C C:LEU164 4.5 34.6 1.0
C8 C:6EY403 4.5 43.0 1.0
CG C:LEU164 4.5 33.7 1.0
ND1 C:HIS192 4.6 42.6 1.0
O C:VAL233 4.7 45.0 1.0
NE C:ARG168 4.7 35.3 1.0
CD2 C:LEU164 4.7 35.7 1.0
CB C:ALA237 4.7 55.8 1.0
O C:LEU164 4.8 38.9 1.0
C4 C:6EY403 4.9 43.4 1.0
NE2 C:HIS192 5.0 39.0 1.0
C C:ASP165 5.0 29.7 1.0

Chlorine binding site 4 out of 4 in 5ixs

Go back to Chlorine Binding Sites List in 5ixs
Chlorine binding site 4 out of 4 in the Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-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 Hydroxylactam Inhibitor Compound 9: (6R)-3-[(2-Chlorophenyl)Sulfanyl]-4-Hydroxy-6-(3-Hydroxyphenyl)-6- (Thiophen-3-Yl)-5,6-Dihydropyridin-2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl802

b:36.5
occ:1.00
 CL D:6EY802 0.0 36.5 1.0
C11 D:6EY802 1.7 36.2 1.0
C10 D:6EY802 2.7 39.5 1.0
C6 D:6EY802 2.8 34.0 1.0
NH2 D:ARG168 3.2 46.2 1.0
S5 D:6EY802 3.3 34.3 1.0
CG D:ASP165 3.3 26.2 1.0
OD2 D:ASP165 3.3 29.4 1.0
CA D:ASP165 3.5 21.8 1.0
OD1 D:ASP165 3.7 24.8 1.0
CB D:ASP165 3.7 24.4 1.0
N D:ASP165 3.8 22.5 1.0
CE1 D:HIS192 4.0 23.3 1.0
O D:HOH926 4.0 31.4 1.0
C9 D:6EY802 4.0 43.2 1.0
C7 D:6EY802 4.0 40.0 1.0
CG1 D:VAL233 4.1 27.2 1.0
CD D:ARG168 4.3 29.4 1.0
CZ D:ARG168 4.4 30.3 1.0
C D:LEU164 4.4 33.7 1.0
O D:VAL233 4.5 42.6 1.0
ND1 D:HIS192 4.5 26.9 1.0
C8 D:6EY802 4.5 35.0 1.0
CG D:LEU164 4.6 34.5 1.0
O D:LEU164 4.8 29.2 1.0
NE D:ARG168 4.8 28.1 1.0
CB D:ALA237 4.8 39.6 1.0
C D:ASP165 4.9 27.7 1.0
CD2 D:LEU164 4.9 32.7 1.0
CB D:LEU164 4.9 28.9 1.0
NE2 D:HIS192 4.9 34.0 1.0
C4 D:6EY802 5.0 34.6 1.0
CA D:GLY193 5.0 26.6 1.0

Reference:

H.E.Purkey, 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, S.S.Labadie, 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, B.Wei, I.Yen, Q.Yue, H.Zhang, A.Zhou. Cell Active Hydroxylactam Inhibitors of Human Lactate Dehydrogenase with Oral Bioavailability in Mice. Acs Med.Chem.Lett. V. 7 896 2016.
ISSN: ISSN 1948-5875
PubMed: 27774125
DOI: 10.1021/ACSMEDCHEMLETT.6B00190
Page generated: Sat Jul 12 03:19:48 2025

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