Atomistry » Chlorine » PDB 5ivr-5j72 » 5ixs
Atomistry »
  Chlorine »
    PDB 5ivr-5j72 »
      5ixs »

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: Fri Jul 26 09:38:25 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy