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Chlorine in PDB 9m3p: Crystal Structure of Human Pyruvate Dehydrogenase Kinase Isoform 1 in Complex with Atp Competitive Inhibitor 3

Enzymatic activity of Crystal Structure of Human Pyruvate Dehydrogenase Kinase Isoform 1 in Complex with Atp Competitive Inhibitor 3

All present enzymatic activity of Crystal Structure of Human Pyruvate Dehydrogenase Kinase Isoform 1 in Complex with Atp Competitive Inhibitor 3:
2.7.11.2;

Protein crystallography data

The structure of Crystal Structure of Human Pyruvate Dehydrogenase Kinase Isoform 1 in Complex with Atp Competitive Inhibitor 3, PDB code: 9m3p was solved by Z.H.Xu, S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.59 / 2.01
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.221, 100.221, 109.815, 90, 90, 90
R / Rfree (%) 16.3 / 19.6

Other elements in 9m3p:

The structure of Crystal Structure of Human Pyruvate Dehydrogenase Kinase Isoform 1 in Complex with Atp Competitive Inhibitor 3 also contains other interesting chemical elements:

Potassium (K) 1 atom
Fluorine (F) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase Isoform 1 in Complex with Atp Competitive Inhibitor 3 (pdb code 9m3p). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase Isoform 1 in Complex with Atp Competitive Inhibitor 3, PDB code: 9m3p:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 9m3p

Go back to Chlorine Binding Sites List in 9m3p
Chlorine binding site 1 out of 2 in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase Isoform 1 in Complex with Atp Competitive Inhibitor 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Pyruvate Dehydrogenase Kinase Isoform 1 in Complex with Atp Competitive Inhibitor 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:41.0
occ:1.00
CL7 A:SZ6502 0.0 41.0 1.0
C5 A:SZ6502 1.7 39.7 1.0
N6 A:SZ6502 2.6 37.5 1.0
N4 A:SZ6502 2.6 38.8 1.0
N A:ALA353 3.3 36.3 1.0
O A:HOH752 3.5 40.4 1.0
CA A:ALA353 3.6 37.4 1.0
CB A:LEU352 3.6 31.0 1.0
CB A:ARG286 3.6 30.3 1.0
CG A:ARG286 3.7 33.0 1.0
C A:LEU352 3.7 39.6 1.0
C1 A:SZ6502 3.8 37.6 1.0
C3 A:SZ6502 3.8 37.5 1.0
CE A:LYS282 3.8 47.9 1.0
CB A:ALA353 3.9 37.2 1.0
CG A:LYS282 3.9 47.9 1.0
O A:LEU352 4.2 33.5 1.0
CA A:LEU352 4.2 31.9 1.0
O A:LYS282 4.3 28.9 1.0
C2 A:SZ6502 4.4 38.6 1.0
CD A:LYS282 4.4 52.9 1.0
CD A:ARG286 4.4 33.9 1.0
OD1 A:ASN283 4.5 31.8 1.0
C A:LYS282 4.8 32.8 1.0
CG A:LEU352 4.9 38.8 1.0
N A:LEU352 4.9 31.5 1.0
CD1 A:LEU352 4.9 37.2 1.0
CA A:ASN283 4.9 30.0 1.0
NZ A:LYS282 5.0 55.5 1.0
C9 A:SZ6502 5.0 29.5 1.0

Chlorine binding site 2 out of 2 in 9m3p

Go back to Chlorine Binding Sites List in 9m3p
Chlorine binding site 2 out of 2 in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase Isoform 1 in Complex with Atp Competitive Inhibitor 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Pyruvate Dehydrogenase Kinase Isoform 1 in Complex with Atp Competitive Inhibitor 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:60.1
occ:1.00
CL7 A:SZ6503 0.0 60.1 1.0
C5 A:SZ6503 1.7 68.3 1.0
N4 A:SZ6503 2.6 68.4 1.0
N6 A:SZ6503 2.6 65.5 1.0
CB A:GLN197 3.7 43.5 1.0
C1 A:SZ6503 3.8 74.5 1.0
C3 A:SZ6503 3.8 70.9 1.0
O A:LEU194 3.9 33.2 1.0
CD2 A:LEU194 4.1 31.7 1.0
CD1 A:LEU79 4.1 30.3 1.0
OG A:SER75 4.1 44.0 1.0
N A:HIS198 4.2 33.4 1.0
CD2 A:LEU79 4.3 34.0 1.0
CA A:LEU194 4.3 39.5 1.0
C2 A:SZ6503 4.4 68.1 1.0
CG A:LEU79 4.5 34.5 1.0
CE1 A:PHE62 4.5 48.2 1.0
C A:LEU194 4.6 37.2 1.0
CB A:HIS198 4.6 34.9 1.0
CG A:GLN197 4.6 48.4 1.0
CB A:LEU194 4.6 29.6 1.0
C A:GLN197 4.7 32.4 1.0
CA A:HIS198 4.7 36.7 1.0
CA A:GLN197 4.8 33.7 1.0
CD1 A:PHE62 4.8 43.6 1.0
C9 A:SZ6503 5.0 66.8 1.0

Reference:

H.Xu, D.Ding, X.Han, K.Miao, C.Liang, H.Yun, W.Zhu, F.Dey, D.Zhao, Y.Wu, M.Reutlinger, J.Yang, G.Zhai, Z.Lin, C.Li, W.Wu, B.Xu, L.Han, S.Chen, X.Huang, F.Casagrande, M.Hilbert, Q.Strebel, M.Wichert, P.Westwood, R.Schafer, D.Roth, D.Heer, X.Tian, T.Ma, T.Zhang, J.Zhao, E.Urich, G.Xia, K.Lassen, H.C.Shen, G.Zou. Discovery of Atp Competitive PDHK1/2 Dual Inhibitors. Bioorg.Med.Chem.Lett. V. 122 30190 2025.
ISSN: ESSN 1464-3405
PubMed: 40107630
DOI: 10.1016/J.BMCL.2025.130190
Page generated: Sun Jul 13 17:12:55 2025

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