Chlorine in PDB 7vbu: Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 5

All present enzymatic activity of Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 5:
2.7.11.2;

The structure of Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 5, PDB code: 7vbu was solved by T.Orita, S.Doi, T.Iwanaga, A.Fujishima, T.Adachi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.80 / 1.89
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	109.462, 109.462, 84.093, 90, 90, 120
R / Rfree (%)	18.5 / 19.7

The binding sites of Chlorine atom in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 5 (pdb code 7vbu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 5, PDB code: 7vbu:

Chlorine binding site 1 out of 1 in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 5


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 2 in Complex with Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:37.7 occ:1.00 OH A:TYR88 3.0 36.2 1.0 ND1 A:HIS123 3.1 42.7 1.0 NE A:ARG162 3.1 47.4 1.0 O A:ACT503 3.2 38.9 1.0 CD A:ARG162 3.3 46.1 1.0 CG2 A:VAL126 3.5 46.1 1.0 CG A:ARG162 3.6 39.7 1.0 CE1 A:TYR88 3.6 38.0 1.0 CZ A:TYR88 3.7 39.0 1.0 CG1 A:VAL126 3.7 41.6 1.0 CB A:HIS123 3.7 41.8 1.0 CB A:VAL126 3.7 43.0 1.0 CH3 A:ACT503 3.8 43.7 1.0 CG A:HIS123 3.8 42.6 1.0 C A:ACT503 3.9 48.2 1.0 CZ A:PHE158 4.2 35.2 1.0 CE1 A:HIS123 4.2 43.3 1.0 CB A:ARG162 4.3 30.4 1.0 CZ A:ARG162 4.4 43.1 1.0 O A:HIS123 4.4 40.6 1.0 CE2 A:PHE158 4.6 39.6 1.0 NH2 A:ARG162 4.8 48.1 1.0 CA A:HIS123 4.8 44.1 1.0 CD1 A:TYR88 4.8 39.6 1.0 CE2 A:TYR88 4.8 38.3 1.0 CE1 A:PHE158 5.0 37.5 1.0

Y.Bessho, T.Akaki, Y.Hara, M.Yamakawa, S.Obika, G.Mori, M.Ubukata, K.Yasue, Y.Nakane, Y.Terasako, T.Orita, S.Doi, T.Iwanaga, A.Fujishima, T.Adachi, H.Ueno, T.Motomura. Structure-Based Drug Design of Novel and Highly Potent Pyruvate Dehydrogenase Kinase Inhibitors. Bioorg.Med.Chem. V. 52 16514 2021.
ISSN: ESSN 1464-3391
DOI: 10.1016/J.BMC.2021.116514