Manganese 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:

Chlorine

(Cl)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total only one binding site of Manganese was 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:

Manganese binding site 1 out of 1 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 Manganese with other atoms in the Mn 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:Mn603 b:15.1 occ:1.00 OE2 A:GLU485 2.1 17.4 1.0 O A:HOH841 2.2 17.9 1.0 NE2 A:HIS483 2.2 13.2 1.0 O A:HOH757 2.3 16.2 1.0 NE2 A:HIS571 2.3 13.2 1.0 N29 A:H6S601 2.3 14.1 0.5 N29 A:H6T602 2.3 15.1 0.5 C28 A:H6T602 3.1 14.7 0.5 CE1 A:HIS483 3.1 14.3 1.0 C28 A:H6S601 3.1 13.2 0.5 CD A:GLU485 3.1 15.9 1.0 CE1 A:HIS571 3.1 12.7 1.0 CD2 A:HIS483 3.2 15.4 1.0 C21 A:H6S601 3.3 14.1 0.5 CD2 A:HIS571 3.3 11.6 1.0 C21 A:H6T602 3.4 14.8 0.5 C20 A:H6S601 3.6 14.2 0.5 OE1 A:GLU485 3.6 17.8 1.0 C20 A:H6T602 3.7 15.5 0.5 O A:HOH817 3.9 31.9 1.0 ND1 A:HIS483 4.2 11.7 1.0 ND1 A:HIS571 4.3 12.6 1.0 CG A:HIS483 4.3 10.5 1.0 O A:HOH761 4.4 41.2 1.0 CG A:GLU485 4.4 13.7 1.0 C27 A:H6T602 4.4 14.9 0.5 CG A:HIS571 4.4 10.4 1.0 C27 A:H6S601 4.5 11.7 0.5 O A:HOH745 4.6 35.2 1.0 C22 A:H6S601 4.6 13.6 0.5 C22 A:H6T602 4.7 15.1 0.5 OG A:SER491 4.8 18.0 1.0 C18 A:H6S601 4.9 14.5 0.5 C17 A:H6T602 4.9 17.2 0.5

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