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Chlorine in PDB 4jnk: Lactate Dehydrogenase A in Complex with Inhibitor Compound 22

Enzymatic activity of Lactate Dehydrogenase A in Complex with Inhibitor Compound 22

All present enzymatic activity of Lactate Dehydrogenase A in Complex with Inhibitor Compound 22:
1.1.1.27;

Protein crystallography data

The structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 22, PDB code: 4jnk was solved by C.Eigenbrot, M.Ultsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.02 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.246, 81.487, 120.414, 90.00, 117.13, 90.00
R / Rfree (%) 15.9 / 20.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lactate Dehydrogenase A in Complex with Inhibitor Compound 22 (pdb code 4jnk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Lactate Dehydrogenase A in Complex with Inhibitor Compound 22, PDB code: 4jnk:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4jnk

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Chlorine binding site 1 out of 6 in the Lactate Dehydrogenase A in Complex with Inhibitor Compound 22


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 Inhibitor Compound 22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl803

b:92.5
occ:0.82
 CL1 A:ZHK803 0.0 92.5 0.8
C29 A:ZHK803 1.7 57.6 0.8
C28 A:ZHK803 2.7 52.8 0.8
C30 A:ZHK803 2.7 55.0 0.8
CD2 A:LEU108 3.0 57.5 1.0
CL2 A:ZHK803 3.1 65.6 0.8
CB A:ARG105 3.1 83.9 1.0
CA A:ARG105 3.2 80.9 1.0
O A:ARG105 3.6 69.5 1.0
C A:ARG105 3.8 74.5 1.0
CB A:LEU108 3.8 58.1 1.0
C27 A:ZHK803 4.0 47.1 0.8
CG A:LEU108 4.0 57.4 1.0
C25 A:ZHK803 4.0 50.1 0.8
NE A:ARG105 4.1 93.7 1.0
CD A:ARG105 4.1 97.3 1.0
CG A:ARG105 4.2 94.2 1.0
CZ A:ARG105 4.2 91.2 1.0
NH1 A:ARG105 4.2 95.3 1.0
O A:SER104 4.4 93.3 1.0
N A:ARG105 4.4 86.8 1.0
C26 A:ZHK803 4.5 44.2 0.8
NH2 A:ARG105 4.8 86.7 1.0
C A:SER104 4.8 91.8 1.0
CG2 A:VAL109 4.9 55.1 1.0

Chlorine binding site 2 out of 6 in 4jnk

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Chlorine binding site 2 out of 6 in the Lactate Dehydrogenase A in Complex with Inhibitor Compound 22


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 Inhibitor Compound 22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl803

b:65.6
occ:0.82
 CL2 A:ZHK803 0.0 65.6 0.8
C28 A:ZHK803 1.7 52.8 0.8
C27 A:ZHK803 2.7 47.1 0.8
C29 A:ZHK803 2.7 57.6 0.8
CL1 A:ZHK803 3.1 92.5 0.8
NH2 A:ARG105 3.6 86.7 1.0
CB A:ARG105 3.8 83.9 1.0
NE A:ARG105 3.8 93.7 1.0
CZ A:ARG105 3.8 91.2 1.0
CG2 A:VAL109 3.8 55.1 1.0
C26 A:ZHK803 4.0 44.2 0.8
C30 A:ZHK803 4.0 55.0 0.8
CB A:PRO138 4.1 23.5 1.0
CG A:PRO138 4.1 30.5 1.0
C25 A:ZHK803 4.5 50.1 0.8
NH1 A:ARG105 4.7 95.3 1.0
CA A:ARG105 4.7 80.9 1.0
O A:ARG105 4.7 69.5 1.0
CD A:ARG105 4.7 97.3 1.0
CD A:PRO138 4.7 25.8 1.0
C A:ARG105 4.8 74.5 1.0
CG A:ARG105 4.8 94.2 1.0
CD2 A:LEU108 4.9 57.5 1.0

Chlorine binding site 3 out of 6 in 4jnk

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Chlorine binding site 3 out of 6 in the Lactate Dehydrogenase A in Complex with Inhibitor Compound 22


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 Inhibitor Compound 22 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl803

b:43.0
occ:1.00
 CL1 C:ZHK803 0.0 43.0 1.0
C29 C:ZHK803 1.7 44.0 1.0
C28 C:ZHK803 2.7 42.5 1.0
C30 C:ZHK803 2.8 34.6 1.0
CL2 C:ZHK803 3.0 38.9 1.0
CD1 C:LEU108 3.5 34.5 1.0
O C:ARG105 3.5 31.6 1.0
CB C:ARG105 3.7 44.0 1.0
CA C:ARG105 3.7 38.3 1.0
CB C:LEU108 3.9 30.5 1.0
CG C:ARG105 3.9 51.2 1.0
CG C:LEU108 3.9 34.5 1.0
C27 C:ZHK803 4.0 39.4 1.0
C C:ARG105 4.0 32.5 1.0
C25 C:ZHK803 4.0 33.9 1.0
CZ C:ARG105 4.3 44.0 1.0
OE1 C:GLN99 4.3 40.5 1.0
CG2 C:VAL109 4.3 28.0 1.0
NE C:ARG105 4.4 49.5 1.0
NH1 C:ARG105 4.4 39.7 1.0
C26 C:ZHK803 4.5 39.1 1.0
NH2 C:ARG105 4.6 41.7 1.0
O C:HOH1195 4.6 44.4 1.0
N C:VAL109 4.7 30.5 1.0
CD C:ARG105 4.7 53.8 1.0
CD C:GLN99 4.8 45.4 1.0
CA C:LEU108 5.0 26.9 1.0

Chlorine binding site 4 out of 6 in 4jnk

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Chlorine binding site 4 out of 6 in the Lactate Dehydrogenase A in Complex with Inhibitor Compound 22


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 Inhibitor Compound 22 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl803

b:38.9
occ:1.00
 CL2 C:ZHK803 0.0 38.9 1.0
C28 C:ZHK803 1.7 42.5 1.0
C29 C:ZHK803 2.7 44.0 1.0
C27 C:ZHK803 2.7 39.4 1.0
CL1 C:ZHK803 3.0 43.0 1.0
NH2 C:ARG105 3.6 41.7 1.0
CG2 C:VAL109 3.6 28.0 1.0
C26 C:ZHK803 4.0 39.1 1.0
C30 C:ZHK803 4.0 34.6 1.0
O C:HOH1161 4.0 44.2 1.0
O C:HOH1057 4.0 43.1 1.0
CB C:PRO138 4.0 24.3 1.0
CZ C:ARG105 4.1 44.0 1.0
CG C:PRO138 4.1 25.1 1.0
NE C:ARG105 4.2 49.5 1.0
C25 C:ZHK803 4.5 33.9 1.0
CD C:PRO138 4.5 24.0 1.0
CB C:ARG105 4.6 44.0 1.0
O C:ARG105 4.7 31.6 1.0
NH1 C:ARG105 4.9 39.7 1.0
C8 C:ZHK803 5.0 22.2 1.0

Chlorine binding site 5 out of 6 in 4jnk

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Chlorine binding site 5 out of 6 in the Lactate Dehydrogenase A in Complex with Inhibitor Compound 22


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Lactate Dehydrogenase A in Complex with Inhibitor Compound 22 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl802

b:0.1
occ:0.79
 CL1 D:ZHK802 0.0 0.1 0.8
C29 D:ZHK802 1.7 73.8 0.8
C28 D:ZHK802 2.7 73.3 0.8
C30 D:ZHK802 2.7 70.9 0.8
OE1 D:GLN99 2.8 66.0 1.0
CD D:GLN99 3.0 60.2 1.0
CL2 D:ZHK802 3.1 59.7 0.8
NE2 D:GLN99 3.3 58.7 1.0
CG D:LEU108 3.6 37.2 1.0
CG D:GLN99 3.7 50.7 1.0
CD1 D:LEU108 3.7 34.0 1.0
CB D:LEU108 3.8 31.8 1.0
CB D:GLN99 3.9 51.2 1.0
C27 D:ZHK802 4.0 70.5 0.8
C25 D:ZHK802 4.0 69.3 0.8
CA D:ARG105 4.4 45.7 1.0
C26 D:ZHK802 4.5 69.2 0.8
CD D:ARG105 4.6 74.7 1.0
CG D:ARG105 4.6 71.0 1.0
N34 D:ZHK802 4.9 64.1 0.8
CB D:ARG105 4.9 57.0 1.0
CD2 D:LEU108 4.9 29.2 1.0
O D:ARG105 5.0 31.0 1.0

Chlorine binding site 6 out of 6 in 4jnk

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Chlorine binding site 6 out of 6 in the Lactate Dehydrogenase A in Complex with Inhibitor Compound 22


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Lactate Dehydrogenase A in Complex with Inhibitor Compound 22 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl802

b:59.7
occ:0.79
 CL2 D:ZHK802 0.0 59.7 0.8
C28 D:ZHK802 1.7 73.3 0.8
C29 D:ZHK802 2.7 73.8 0.8
C27 D:ZHK802 2.7 70.5 0.8
CD D:ARG105 2.8 74.7 1.0
CL1 D:ZHK802 3.1 0.1 0.8
NH1 D:ARG105 3.2 81.2 1.0
NE D:ARG105 3.6 78.7 1.0
CG D:ARG105 3.7 71.0 1.0
CZ D:ARG105 3.8 82.5 1.0
CG D:PRO138 3.8 28.4 1.0
C26 D:ZHK802 4.0 69.2 0.8
C30 D:ZHK802 4.0 70.9 0.8
CB D:PRO138 4.0 22.6 1.0
CB D:ARG105 4.0 57.0 1.0
CD D:PRO138 4.4 25.0 1.0
CA D:ARG105 4.4 45.7 1.0
C25 D:ZHK802 4.5 69.3 0.8
CG2 D:VAL109 4.7 30.3 1.0
O13 D:ZHK802 4.7 26.9 0.8
C8 D:ZHK802 4.9 28.3 0.8
O D:ARG105 4.9 31.0 1.0
CD1 D:LEU108 4.9 34.0 1.0

Reference:

P.S.Dragovich, B.P.Fauber, L.B.Corson, C.Z.Ding, C.Eigenbrot, H.Ge, A.M.Giannetti, T.Hunsaker, S.Labadie, Y.Liu, S.Malek, B.Pan, D.Peterson, K.Pitts, H.E.Purkey, S.Sideris, M.Ultsch, E.Vanderporten, B.Wei, Q.Xu, I.Yen, Q.Yue, H.Zhang, X.Zhang. Identification of Substituted 2-Thio-6-Oxo-1,6-Dihydropyrimidines As Inhibitors of Human Lactate Dehydrogenase. Bioorg.Med.Chem.Lett. V. 23 3186 2013.
ISSN: ISSN 0960-894X
PubMed: 23628333
DOI: 10.1016/J.BMCL.2013.04.001
Page generated: Sun Jul 21 17:35:52 2024

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