Manganese in PDB 6bgy: Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound 46)

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound 46), PDB code: 6bgy 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)	30.97 / 1.22
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.685, 61.943, 46.747, 90.00, 92.22, 90.00
R / Rfree (%)	16.6 / 19.3

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound 46) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound 46) (pdb code 6bgy). 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 2-((2-Chlorophenyl)(2- (1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound 46), PDB code: 6bgy:

Manganese binding site 1 out of 1 in the Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound 46)


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 2-((2-Chlorophenyl)(2- (1-Methylpyrrolidin-2-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound 46) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:13.8 occ:1.00 OE2 A:GLU485 2.1 17.9 1.0 O A:HOH773 2.2 19.5 1.0 O A:HOH726 2.2 14.5 1.0 NE2 A:HIS483 2.2 14.2 1.0 N29 A:DLJ601 2.3 12.4 1.0 NE2 A:HIS571 2.3 12.8 1.0 CE1 A:HIS483 3.1 13.2 1.0 CD A:GLU485 3.1 14.4 1.0 C28 A:DLJ601 3.1 12.4 1.0 CE1 A:HIS571 3.2 12.1 1.0 C21 A:DLJ601 3.2 12.5 1.0 CD2 A:HIS483 3.3 14.1 1.0 CD2 A:HIS571 3.3 12.2 1.0 OE1 A:GLU485 3.5 17.6 1.0 C20 A:DLJ601 3.6 13.9 1.0 O A:HOH849 4.3 29.0 1.0 ND1 A:HIS483 4.3 13.5 1.0 ND1 A:HIS571 4.3 11.3 1.0 O A:HOH831 4.4 31.6 1.0 CG A:HIS483 4.4 12.1 1.0 CG A:HIS571 4.4 11.8 1.0 CG A:GLU485 4.5 14.0 1.0 C27 A:DLJ601 4.5 12.2 1.0 C22 A:DLJ601 4.5 12.8 1.0 OG A:SER491 4.6 16.6 1.0 C17 A:DLJ601 4.9 34.5 1.0 C18 A:DLJ601 5.0 13.7 1.0

J.R.Horton, X.Liu, L.Wu, K.Zhang, J.Shanks, X.Zhang, G.Rai, B.T.Mott, D.J.Jansen, S.C.Kales, M.J.Henderson, K.Pohida, Y.Fang, X.Hu, A.Jadhav, D.J.Maloney, M.D.Hall, A.Simeonov, H.Fu, P.M.Vertino, Q.Yan, X.Cheng. Insights Into the Action of Inhibitor Enantiomers Against Histone Lysine Demethylase 5A. J. Med. Chem. V. 61 3193 2018.
ISSN: ISSN 1520-4804
PubMed: 29537847
DOI: 10.1021/ACS.JMEDCHEM.8B00261