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Chlorine in PDB 4zvv: Lactate Dehydrogenase A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140

Enzymatic activity of Lactate Dehydrogenase A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140

All present enzymatic activity of Lactate Dehydrogenase A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140:
1.1.1.27;

Protein crystallography data

The structure of Lactate Dehydrogenase A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140, PDB code: 4zvv was solved by Y.Li, Z.Chen, C.Eigenbrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.45 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.164, 81.288, 102.470, 90.00, 98.31, 90.00
R / Rfree (%) 23.2 / 25.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lactate Dehydrogenase A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140 (pdb code 4zvv). 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 A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140, PDB code: 4zvv:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4zvv

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Chlorine binding site 1 out of 4 in the Lactate Dehydrogenase A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lactate Dehydrogenase A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:38.3
occ:1.00
 CL A:GN0405 0.0 38.3 1.0
C27 A:GN0405 1.7 36.2 1.0
C22 A:GN0405 2.7 35.5 1.0
C26 A:GN0405 2.7 36.1 1.0
S21 A:GN0405 3.1 35.0 1.0
NH2 A:ARG168 3.1 32.7 1.0
OD2 A:ASP165 3.4 31.0 1.0
CG A:ASP165 3.5 30.9 1.0
CA A:ASP165 3.8 30.5 1.0
OD1 A:ASP165 3.8 31.4 1.0
O A:HOH513 3.9 38.8 1.0
C25 A:GN0405 4.0 35.7 1.0
C23 A:GN0405 4.0 35.6 1.0
N A:ASP165 4.0 30.6 1.0
CE1 A:HIS192 4.0 32.8 1.0
CG1 A:VAL233 4.0 37.6 1.0
CB A:ASP165 4.1 30.6 1.0
CD A:ARG168 4.1 31.5 1.0
CZ A:ARG168 4.3 32.1 1.0
C24 A:GN0405 4.5 35.4 1.0
ND1 A:HIS192 4.5 32.4 1.0
C A:LEU164 4.5 30.8 1.0
CG A:LEU164 4.5 31.0 1.0
CD2 A:LEU164 4.6 30.7 1.0
NE A:ARG168 4.7 31.9 1.0
C16 A:GN0405 4.7 34.8 1.0
O A:LEU164 4.8 30.6 1.0
CB A:LEU164 4.8 31.0 1.0
CA A:GLY193 4.9 33.2 1.0
CB A:ALA237 4.9 36.4 1.0
NE2 A:HIS192 5.0 33.0 1.0
N A:GLY193 5.0 33.0 1.0
O A:VAL233 5.0 37.5 1.0

Chlorine binding site 2 out of 4 in 4zvv

Go back to Chlorine Binding Sites List in 4zvv
Chlorine binding site 2 out of 4 in the Lactate Dehydrogenase A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lactate Dehydrogenase A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:35.8
occ:1.00
 CL B:GN0404 0.0 35.8 1.0
C27 B:GN0404 1.7 35.2 1.0
C26 B:GN0404 2.7 35.6 1.0
C22 B:GN0404 2.7 35.4 1.0
S21 B:GN0404 3.1 35.1 1.0
NH2 B:ARG168 3.3 31.6 1.0
OD2 B:ASP165 3.4 32.9 1.0
CG B:ASP165 3.5 32.1 1.0
CA B:ASP165 3.8 31.3 1.0
OD1 B:ASP165 3.8 32.9 1.0
N B:ASP165 3.9 31.5 1.0
C25 B:GN0404 4.0 35.5 1.0
C23 B:GN0404 4.0 35.3 1.0
CE1 B:HIS192 4.0 32.6 1.0
CB B:ASP165 4.1 31.4 1.0
CD B:ARG168 4.2 30.2 1.0
CG1 B:VAL233 4.3 37.2 1.0
CG B:LEU164 4.4 31.8 1.0
CZ B:ARG168 4.4 31.4 1.0
C B:LEU164 4.4 31.6 1.0
C24 B:GN0404 4.5 35.4 1.0
CD2 B:LEU164 4.5 31.6 1.0
ND1 B:HIS192 4.6 32.4 1.0
O B:LEU164 4.7 31.6 1.0
CB B:ALA237 4.7 34.9 1.0
NE2 B:HIS192 4.8 32.9 1.0
NE B:ARG168 4.8 31.3 1.0
CB B:LEU164 4.8 31.8 1.0
C16 B:GN0404 4.8 35.5 1.0
O B:VAL233 4.9 36.6 1.0

Chlorine binding site 3 out of 4 in 4zvv

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Chlorine binding site 3 out of 4 in the Lactate Dehydrogenase A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lactate Dehydrogenase A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:38.2
occ:1.00
 CL C:GN0403 0.0 38.2 1.0
C27 C:GN0403 1.7 36.1 1.0
C26 C:GN0403 2.7 36.0 1.0
C22 C:GN0403 2.7 35.9 1.0
S21 C:GN0403 3.2 34.9 1.0
NH2 C:ARG168 3.2 34.6 1.0
CG C:ASP165 3.5 29.3 1.0
OD2 C:ASP165 3.5 29.9 1.0
OD1 C:ASP165 3.7 30.1 1.0
CA C:ASP165 3.8 28.5 1.0
C25 C:GN0403 4.0 36.1 1.0
CB C:ASP165 4.0 28.5 1.0
C23 C:GN0403 4.0 35.9 1.0
CE1 C:HIS192 4.0 30.5 1.0
O C:HOH508 4.0 33.4 1.0
N C:ASP165 4.0 28.7 1.0
CG1 C:VAL233 4.1 35.7 1.0
CD C:ARG168 4.3 31.5 1.0
CZ C:ARG168 4.3 34.0 1.0
C24 C:GN0403 4.5 36.1 1.0
ND1 C:HIS192 4.6 30.5 1.0
C C:LEU164 4.6 28.8 1.0
CG C:LEU164 4.7 28.9 1.0
CD2 C:LEU164 4.7 28.5 1.0
NE C:ARG168 4.7 33.3 1.0
NE2 C:HIS192 4.8 30.5 1.0
O C:VAL233 4.8 35.8 1.0
CB C:ALA237 4.8 34.5 1.0
C16 C:GN0403 4.8 35.6 1.0
O C:LEU164 5.0 28.5 1.0
CA C:GLY193 5.0 31.8 1.0

Chlorine binding site 4 out of 4 in 4zvv

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Chlorine binding site 4 out of 4 in the Lactate Dehydrogenase A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lactate Dehydrogenase A in Complex with A Trisubstituted Piperidine-2, 4-Dione Inhibitor Gne-140 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:35.9
occ:1.00
 CL D:GN0403 0.0 35.9 1.0
C27 D:GN0403 1.7 35.1 1.0
C26 D:GN0403 2.7 35.0 1.0
C22 D:GN0403 2.7 34.6 1.0
S21 D:GN0403 3.2 35.2 1.0
OD2 D:ASP165 3.4 28.3 1.0
NH2 D:ARG168 3.5 30.6 1.0
CG D:ASP165 3.5 28.1 1.0
CA D:ASP165 3.8 27.8 1.0
OD1 D:ASP165 3.8 27.9 1.0
O D:HOH505 3.9 38.7 1.0
C25 D:GN0403 4.0 35.0 1.0
C23 D:GN0403 4.0 34.8 1.0
CB D:ASP165 4.0 27.9 1.0
N D:ASP165 4.0 27.7 1.0
CE1 D:HIS192 4.1 32.1 1.0
CG1 D:VAL233 4.2 35.9 1.0
CD D:ARG168 4.4 29.0 1.0
C24 D:GN0403 4.5 35.0 1.0
C D:LEU164 4.6 27.5 1.0
ND1 D:HIS192 4.6 32.3 1.0
CZ D:ARG168 4.6 30.6 1.0
CB D:ALA237 4.7 33.5 1.0
CA D:GLY193 4.8 32.4 1.0
CG D:LEU164 4.8 26.8 1.0
O D:VAL233 4.8 35.8 1.0
C16 D:GN0403 4.8 33.6 1.0
CD2 D:LEU164 4.9 26.3 1.0
O D:LEU164 4.9 27.5 1.0
CB D:LEU164 5.0 27.2 1.0

Reference:

A.Boudreau, H.E.Purkey, A.Hitz, K.Robarge, D.Peterson, S.Labadie, M.Kwong, R.Hong, M.Gao, C.Del Nagro, R.Pusapati, S.Ma, L.Salphati, J.Pang, A.Zhou, T.Lai, Y.Li, Z.Chen, B.Wei, I.Yen, S.Sideris, M.Mccleland, R.Firestein, L.Corson, A.Vanderbilt, S.Williams, A.Daemen, M.Belvin, C.Eigenbrot, P.K.Jackson, S.Malek, G.Hatzivassiliou, D.Sampath, M.Evangelista, T.O'brien. Metabolic Plasticity Underpins Innate and Acquired Resistance to Ldha Inhibition. Nat.Chem.Biol. V. 12 779 2016.
ISSN: ESSN 1552-4469
PubMed: 27479743
DOI: 10.1038/NCHEMBIO.2143
Page generated: Fri Jul 26 04:51:40 2024

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