Chlorine in PDB 6dq8: Linked KDM5A Jmj Domain Bound to the Inhibitor N49 I.E. 2-((2- Chlorophenyl)(2-(1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N49 I.E. 2-((2- Chlorophenyl)(2-(1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid, PDB code: 6dq8 was solved by J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.01 / 1.46
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.253, 61.754, 46.718, 90.00, 92.33, 90.00
R / Rfree (%)	18.6 / 21

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N49 I.E. 2-((2- Chlorophenyl)(2-(1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Chlorine atom in the Linked KDM5A Jmj Domain Bound to the Inhibitor N49 I.E. 2-((2- Chlorophenyl)(2-(1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid (pdb code 6dq8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Linked KDM5A Jmj Domain Bound to the Inhibitor N49 I.E. 2-((2- Chlorophenyl)(2-(1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid, PDB code: 6dq8:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N49 I.E. 2-((2- Chlorophenyl)(2-(1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Linked KDM5A Jmj Domain Bound to the Inhibitor N49 I.E. 2-((2- Chlorophenyl)(2-(1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:21.0 occ:0.50 CL A:H6S601 0.0 21.0 0.5 C06 A:H6T602 0.8 21.0 0.5 C05 A:H6T602 1.5 19.9 0.5 C02 A:H6S601 1.7 16.8 0.5 C07 A:H6T602 2.0 18.1 0.5 C04 A:H6T602 2.7 20.8 0.5 C03 A:H6S601 2.7 16.6 0.5 C07 A:H6S601 2.7 18.3 0.5 O09 A:H6S601 2.8 22.1 0.5 C08 A:H6T602 3.0 16.4 0.5 C02 A:H6T602 3.0 20.0 0.5 C08 A:H6S601 3.2 18.2 0.5 C03 A:H6T602 3.2 21.4 0.5 S19 A:H6S601 3.4 14.0 0.5 S19 A:H6T602 3.4 16.7 0.5 C10 A:H6S601 3.5 23.0 0.5 C18 A:H6T602 3.6 14.5 0.5 CB A:ALA411 3.7 19.9 1.0 C18 A:H6S601 3.7 14.5 0.5 NH1 A:ARG73 4.0 32.4 1.0 C04 A:H6S601 4.0 18.2 0.5 C06 A:H6S601 4.0 17.3 0.5 CZ A:ARG73 4.1 37.7 1.0 O09 A:H6T602 4.2 17.1 0.5 CD2 A:TYR409 4.3 14.4 1.0 CE2 A:TYR409 4.4 15.3 1.0 C11 A:H6S601 4.4 24.9 0.5 NE A:ARG73 4.4 26.5 1.0 CB A:PHE480 4.4 15.1 1.0 O A:SER479 4.5 12.7 1.0 NH2 A:ARG73 4.5 38.0 1.0 C05 A:H6S601 4.5 18.9 0.5 CL A:H6T602 4.6 22.5 0.5 CD A:ARG73 4.7 24.2 1.0 O A:HOH876 4.7 44.4 1.0 NE2 A:GLN75 4.8 15.7 1.0 C20 A:H6T602 4.9 15.5 0.5 CE1 A:TYR472 4.9 18.0 1.0 CA A:PHE480 5.0 11.4 1.0

Chlorine binding site 2 out of 2 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N49 I.E. 2-((2- Chlorophenyl)(2-(1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Linked KDM5A Jmj Domain Bound to the Inhibitor N49 I.E. 2-((2- Chlorophenyl)(2-(1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl602 b:22.5 occ:0.50 CL A:H6T602 0.0 22.5 0.5 C06 A:H6S601 0.8 17.3 0.5 C05 A:H6S601 1.7 18.9 0.5 C02 A:H6T602 1.7 20.0 0.5 C07 A:H6S601 1.9 18.3 0.5 C03 A:H6T602 2.7 21.4 0.5 C07 A:H6T602 2.7 18.1 0.5 C08 A:H6S601 2.8 18.2 0.5 C04 A:H6S601 2.8 18.2 0.5 O09 A:H6T602 2.9 17.1 0.5 C02 A:H6S601 3.0 16.8 0.5 C08 A:H6T602 3.1 16.4 0.5 C03 A:H6S601 3.3 16.6 0.5 C18 A:H6S601 3.3 14.5 0.5 O A:HOH897 3.4 39.2 1.0 ND1 A:HIS483 3.5 11.7 1.0 C18 A:H6T602 3.5 14.5 0.5 C20 A:H6S601 3.7 14.2 0.5 C20 A:H6T602 3.7 15.5 0.5 O A:HOH896 3.7 37.6 1.0 CE1 A:HIS483 3.7 14.3 1.0 C04 A:H6T602 4.0 20.8 0.5 C06 A:H6T602 4.0 21.0 0.5 CB A:PHE480 4.0 15.1 1.0 CG A:HIS483 4.0 10.5 1.0 O09 A:H6S601 4.1 22.1 0.5 O A:CYS481 4.1 14.8 1.0 C17 A:H6T602 4.2 17.2 0.5 C10 A:H6T602 4.3 21.0 0.5 N A:CYS481 4.3 15.7 1.0 NE2 A:HIS483 4.4 13.2 1.0 C05 A:H6T602 4.5 19.9 0.5 CD2 A:HIS483 4.5 15.4 1.0 C10 A:H6S601 4.5 23.0 0.5 CA A:PHE480 4.6 11.4 1.0 CL A:H6S601 4.6 21.0 0.5 CB A:HIS483 4.6 13.1 1.0 C12 A:H6T602 4.6 21.6 0.5 S19 A:H6S601 4.6 14.0 0.5 SG A:CYS481 4.7 20.6 1.0 O A:HOH876 4.7 44.4 1.0 C A:PHE480 4.7 14.9 1.0 C21 A:H6T602 4.8 14.8 0.5 S19 A:H6T602 4.8 16.7 0.5 C21 A:H6S601 4.8 14.1 0.5 O A:GLN535 4.8 22.3 1.0 C11 A:H6T602 4.9 21.5 0.5 C A:CYS481 4.9 15.0 1.0

J.R.Horton, C.B.Woodcock, Q.Chen, X.Liu, X.Zhang, J.Shanks, G.Rai, B.T.Mott, D.J.Jansen, S.C.Kales, M.J.Henderson, M.Cyr, K.Pohida, X.Hu, P.Shah, X.Xu, A.Jadhav, D.J.Maloney, M.D.Hall, A.Simeonov, H.Fu, P.M.Vertino, X.Cheng. Structure-Based Engineering of Irreversible Inhibitors Against Histone Lysine Demethylase KDM5A. J. Med. Chem. V. 61 10588 2018.
ISSN: ISSN 1520-4804
PubMed: 30392349
DOI: 10.1021/ACS.JMEDCHEM.8B01219