Atomistry » Chlorine » PDB 5ivs-5j7f » 5ixy
Atomistry »
  Chlorine »
    PDB 5ivs-5j7f »
      5ixy »

Chlorine in PDB 5ixy: Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-One

Enzymatic activity of Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-One

All present enzymatic activity of Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-One:
1.1.1.27;

Protein crystallography data

The structure of Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-One, PDB code: 5ixy 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) 33.10 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.452, 80.696, 102.236, 90.00, 97.90, 90.00
R / Rfree (%) 23.6 / 27.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-One (pdb code 5ixy). 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 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-One, PDB code: 5ixy:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5ixy

Go back to Chlorine Binding Sites List in 5ixy
Chlorine binding site 1 out of 4 in the Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-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 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:58.7
occ:1.00
CL A:GN2404 0.0 58.7 1.0
C27 A:GN2404 1.7 58.6 1.0
C26 A:GN2404 2.7 58.4 1.0
C22 A:GN2404 2.7 58.1 1.0
NH2 A:ARG168 3.1 58.2 1.0
S21 A:GN2404 3.2 59.0 1.0
CG A:ASP165 3.4 60.7 1.0
OD2 A:ASP165 3.5 68.5 1.0
OD1 A:ASP165 3.6 60.6 1.0
CA A:ASP165 3.7 46.4 1.0
N A:ASP165 3.9 47.4 1.0
C25 A:GN2404 4.0 57.5 1.0
C23 A:GN2404 4.0 56.6 1.0
CB A:ASP165 4.0 48.6 1.0
CE1 A:HIS192 4.2 56.5 1.0
CD A:ARG168 4.3 52.5 1.0
CG1 A:VAL233 4.3 50.2 1.0
CZ A:ARG168 4.4 74.1 1.0
C A:LEU164 4.5 52.6 1.0
C24 A:GN2404 4.5 56.6 1.0
ND1 A:HIS192 4.6 57.2 1.0
CG A:LEU164 4.7 54.7 1.0
O A:LEU164 4.7 52.6 1.0
CB A:ALA237 4.8 46.4 1.0
CD2 A:LEU164 4.8 57.2 1.0
C16 A:GN2404 4.8 58.4 1.0
NE A:ARG168 4.8 60.3 1.0
CB A:LEU164 4.8 50.0 1.0
O A:VAL233 5.0 49.7 1.0

Chlorine binding site 2 out of 4 in 5ixy

Go back to Chlorine Binding Sites List in 5ixy
Chlorine binding site 2 out of 4 in the Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-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 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:54.9
occ:1.00
CL B:GN2405 0.0 54.9 1.0
C27 B:GN2405 1.7 56.5 1.0
C26 B:GN2405 2.7 56.9 1.0
C22 B:GN2405 2.7 57.3 1.0
NH2 B:ARG168 3.1 47.0 1.0
S21 B:GN2405 3.1 59.0 1.0
CG B:ASP165 3.4 56.6 1.0
OD1 B:ASP165 3.6 58.3 1.0
OD2 B:ASP165 3.6 60.3 1.0
CA B:ASP165 3.7 43.3 1.0
N B:ASP165 3.9 44.8 1.0
C25 B:GN2405 4.0 56.9 1.0
C23 B:GN2405 4.0 56.8 1.0
CB B:ASP165 4.0 45.2 1.0
CE1 B:HIS192 4.2 51.3 1.0
CD B:ARG168 4.3 48.0 1.0
CG1 B:VAL233 4.3 50.0 1.0
CZ B:ARG168 4.3 61.7 1.0
C B:LEU164 4.4 50.6 1.0
C24 B:GN2405 4.5 57.0 1.0
ND1 B:HIS192 4.7 51.9 1.0
CG B:LEU164 4.7 52.7 1.0
O B:LEU164 4.7 51.0 1.0
CB B:ALA237 4.7 48.2 1.0
NE B:ARG168 4.8 51.7 1.0
CD2 B:LEU164 4.8 55.4 1.0
C16 B:GN2405 4.8 55.8 1.0
CB B:LEU164 4.8 48.2 1.0
O B:VAL233 4.9 49.1 1.0

Chlorine binding site 3 out of 4 in 5ixy

Go back to Chlorine Binding Sites List in 5ixy
Chlorine binding site 3 out of 4 in the Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-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 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:71.7
occ:1.00
CL C:GN2404 0.0 71.7 1.0
C27 C:GN2404 1.7 70.8 1.0
C26 C:GN2404 2.7 70.4 1.0
C22 C:GN2404 2.7 70.3 1.0
S21 C:GN2404 3.2 69.7 1.0
NH2 C:ARG168 3.3 78.1 1.0
CG C:ASP165 3.5 52.8 1.0
OD2 C:ASP165 3.6 56.7 1.0
OD1 C:ASP165 3.7 54.0 1.0
CA C:ASP165 3.9 39.4 1.0
C25 C:GN2404 4.0 70.3 1.0
C23 C:GN2404 4.0 70.4 1.0
CB C:ASP165 4.1 41.7 1.0
N C:ASP165 4.1 39.9 1.0
CG1 C:VAL233 4.2 53.3 1.0
CE1 C:HIS192 4.3 56.5 1.0
CD C:ARG168 4.4 63.2 1.0
CZ C:ARG168 4.5 91.8 1.0
C24 C:GN2404 4.5 70.4 1.0
CB C:ALA237 4.6 54.5 1.0
C C:LEU164 4.6 44.1 1.0
ND1 C:HIS192 4.7 57.3 1.0
C16 C:GN2404 4.8 66.1 1.0
O C:VAL233 4.9 53.8 1.0
NE C:ARG168 4.9 75.9 1.0
O C:LEU164 4.9 44.0 1.0
CG C:LEU164 4.9 45.0 1.0
CD2 C:LEU164 5.0 47.6 1.0
CA C:GLY193 5.0 53.9 1.0

Chlorine binding site 4 out of 4 in 5ixy

Go back to Chlorine Binding Sites List in 5ixy
Chlorine binding site 4 out of 4 in the Lactate Dehydrogenase in Complex with Hydroxylactam Inhibitor Compound 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-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 31: (2~{S})-5-(2-Chlorophenyl)Sulfanyl-2-(4-Morpholin-4-Ylphenyl)-4- Oxidanyl-2-Thiophen-3-Yl-1,3-Dihydropyridin-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:64.9
occ:1.00
CL D:GN2402 0.0 64.9 1.0
C27 D:GN2402 1.7 63.5 1.0
C26 D:GN2402 2.7 62.3 1.0
C22 D:GN2402 2.7 62.5 1.0
S21 D:GN2402 3.2 62.9 1.0
NH2 D:ARG168 3.2 58.4 1.0
CG D:ASP165 3.5 59.0 1.0
OD2 D:ASP165 3.5 66.9 1.0
OD1 D:ASP165 3.7 59.6 1.0
CA D:ASP165 3.9 41.7 1.0
C25 D:GN2402 4.0 61.5 1.0
C23 D:GN2402 4.0 61.0 1.0
CB D:ASP165 4.1 43.9 1.0
N D:ASP165 4.1 42.4 1.0
CG1 D:VAL233 4.3 50.6 1.0
CE1 D:HIS192 4.3 49.9 1.0
CD D:ARG168 4.4 46.5 1.0
CZ D:ARG168 4.5 69.2 1.0
C24 D:GN2402 4.5 61.0 1.0
CB D:ALA237 4.6 48.5 1.0
C D:LEU164 4.7 46.0 1.0
ND1 D:HIS192 4.7 50.8 1.0
C16 D:GN2402 4.8 59.9 1.0
O D:VAL233 4.9 51.7 1.0
NE D:ARG168 4.9 53.8 1.0
CG D:LEU164 4.9 46.1 1.0
O D:LEU164 4.9 45.7 1.0
CD2 D:LEU164 5.0 48.0 1.0
CA D:GLY193 5.0 47.4 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 09:38:27 2024

Last articles

Cl in 4LFV
Cl in 4LFU
Cl in 4LFP
Cl in 4LER
Cl in 4LDV
Cl in 4LES
Cl in 4LEQ
Cl in 4LE7
Cl in 4LDY
Cl in 4LDW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy