Manganese in PDB 6dq9: Linked KDM5A Jmj Domain Bound to the Covalent Inhibitor N69 I.E. [2- ((3-Acrylamidophenyl)(2-(Piperidin-1-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid]

The structure of Linked KDM5A Jmj Domain Bound to the Covalent Inhibitor N69 I.E. [2- ((3-Acrylamidophenyl)(2-(Piperidin-1-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid], PDB code: 6dq9 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)	33.10 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.517, 62.001, 46.725, 90.00, 92.13, 90.00
R / Rfree (%)	17.4 / 19.8

The binding sites of Manganese atom in the Linked KDM5A Jmj Domain Bound to the Covalent Inhibitor N69 I.E. [2- ((3-Acrylamidophenyl)(2-(Piperidin-1-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid] (pdb code 6dq9). 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 Covalent Inhibitor N69 I.E. [2- ((3-Acrylamidophenyl)(2-(Piperidin-1-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid], PDB code: 6dq9:

Manganese binding site 1 out of 1 in the Linked KDM5A Jmj Domain Bound to the Covalent Inhibitor N69 I.E. [2- ((3-Acrylamidophenyl)(2-(Piperidin-1-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 Covalent Inhibitor N69 I.E. [2- ((3-Acrylamidophenyl)(2-(Piperidin-1-Yl)Ethoxy)Methyl)Thieno[3,2- B]Pyridine-7-Carboxylic Acid] within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:14.6 occ:1.00 O A:HOH830 2.1 20.2 1.0 OE1 A:GLU485 2.1 18.2 1.0 NE2 A:HIS483 2.2 13.0 1.0 O A:HOH719 2.2 20.3 1.0 NE2 A:HIS571 2.2 18.5 1.0 N31 A:H74601 2.3 15.6 1.0 CE1 A:HIS571 3.1 18.1 1.0 C32 A:H74601 3.1 16.1 1.0 CE1 A:HIS483 3.1 13.3 1.0 CD A:GLU485 3.2 18.5 1.0 CD2 A:HIS483 3.2 14.7 1.0 C06 A:H74601 3.3 13.5 1.0 CD2 A:HIS571 3.3 14.4 1.0 OE2 A:GLU485 3.6 21.0 1.0 C07 A:H74601 3.7 15.1 1.0 O A:HOH728 4.1 38.1 1.0 ND1 A:HIS483 4.2 13.6 1.0 O A:HOH853 4.2 42.5 1.0 ND1 A:HIS571 4.2 17.2 1.0 CG A:HIS483 4.3 11.1 1.0 CG A:HIS571 4.4 13.3 1.0 CG A:GLU485 4.4 17.6 1.0 C33 A:H74601 4.4 12.4 1.0 C05 A:H74601 4.6 12.8 1.0 OG A:SER491 4.7 18.9 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