Chlorine in PDB 6bgv: Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (Piperidin-1-Yl)Ethoxy)Methyl)-1L2-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid (Compound N40)

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (Piperidin-1-Yl)Ethoxy)Methyl)-1L2-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid (Compound N40), PDB code: 6bgv 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)	30.94 / 1.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.289, 61.883, 46.735, 90.00, 92.32, 90.00
R / Rfree (%)	16.8 / 18.4

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (Piperidin-1-Yl)Ethoxy)Methyl)-1L2-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid (Compound N40) 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 2-((2-Chlorophenyl)(2- (Piperidin-1-Yl)Ethoxy)Methyl)-1L2-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid (Compound N40) (pdb code 6bgv). 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 2-((2-Chlorophenyl)(2- (Piperidin-1-Yl)Ethoxy)Methyl)-1L2-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid (Compound N40), PDB code: 6bgv:
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 2-((2-Chlorophenyl)(2- (Piperidin-1-Yl)Ethoxy)Methyl)-1L2-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid (Compound N40)


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 2-((2-Chlorophenyl)(2- (Piperidin-1-Yl)Ethoxy)Methyl)-1L2-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid (Compound N40) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:13.2 occ:0.50 CL1 A:DQG601 0.0 13.2 0.5 C09 A:DQG601 1.0 18.5 0.5 C10 A:DQG601 1.6 17.9 0.5 C13 A:DQG601 1.7 13.9 0.5 C08 A:DQG601 2.2 13.2 0.5 C12 A:DQG601 2.7 15.4 0.5 C08 A:DQG601 2.7 15.7 0.5 C11 A:DQG601 2.9 13.2 0.5 C07 A:DQG601 3.1 14.8 0.5 C07 A:DQG601 3.1 14.6 0.5 C13 A:DQG601 3.2 19.0 0.5 CB A:ALA411 3.4 15.1 1.0 N05 A:DQG601 3.5 9.3 1.0 C12 A:DQG601 3.5 15.9 0.5 C06 A:DQG601 3.6 11.2 1.0 CE2 A:TYR409 3.8 10.4 1.0 CD2 A:TYR409 3.9 9.6 1.0 C11 A:DQG601 4.0 17.2 0.5 C09 A:DQG601 4.0 16.3 0.5 NH1 A:ARG73 4.1 24.2 1.0 CE2 A:TYR472 4.1 11.2 1.0 O15 A:DQG601 4.2 22.3 1.0 O A:SER479 4.3 9.7 1.0 CZ A:ARG73 4.3 26.1 1.0 C16 A:DQG601 4.3 32.8 1.0 CB A:PHE480 4.4 12.8 1.0 O01 A:DQG601 4.4 9.8 1.0 C10 A:DQG601 4.5 19.1 0.5 CD2 A:TYR472 4.5 11.2 1.0 NE A:ARG73 4.7 17.7 1.0 OD1 A:ASP412 4.7 31.9 1.0 NH2 A:ARG73 4.7 31.7 1.0 CA A:ALA411 4.7 14.5 1.0 C04 A:DQG601 4.8 8.2 1.0 CZ A:TYR409 4.8 10.4 1.0 CL1 A:DQG601 4.8 23.4 0.5 CA A:PHE480 4.8 9.0 1.0 CD A:ARG73 4.9 17.7 1.0 NE2 A:GLN75 4.9 14.3 1.0 CG A:TYR409 5.0 11.9 1.0

Chlorine binding site 2 out of 2 in the Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (Piperidin-1-Yl)Ethoxy)Methyl)-1L2-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid (Compound N40)


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 2-((2-Chlorophenyl)(2- (Piperidin-1-Yl)Ethoxy)Methyl)-1L2-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid (Compound N40) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:23.4 occ:0.50 CL1 A:DQG601 0.0 23.4 0.5 C09 A:DQG601 0.9 16.3 0.5 C10 A:DQG601 1.7 19.1 0.5 C13 A:DQG601 1.7 19.0 0.5 C08 A:DQG601 2.2 15.7 0.5 C12 A:DQG601 2.7 15.9 0.5 C08 A:DQG601 2.7 13.2 0.5 C07 A:DQG601 3.0 14.8 0.5 C11 A:DQG601 3.0 17.2 0.5 O15 A:DQG601 3.0 22.3 1.0 C07 A:DQG601 3.1 14.6 0.5 O A:HOH895 3.2 30.8 1.0 C13 A:DQG601 3.3 13.9 0.5 C06 A:DQG601 3.4 11.2 1.0 C12 A:DQG601 3.6 15.4 0.5 C26 A:DQG601 3.7 13.4 1.0 ND1 A:HIS483 3.8 10.7 1.0 C16 A:DQG601 3.8 32.8 1.0 C11 A:DQG601 4.0 13.2 0.5 C09 A:DQG601 4.0 18.5 0.5 CE1 A:HIS483 4.1 10.6 1.0 O A:CYS481 4.2 11.3 1.0 CG A:HIS483 4.2 8.5 1.0 O A:GLN535 4.3 20.3 1.0 CB A:PHE480 4.3 12.8 1.0 N A:CYS481 4.4 11.9 1.0 N05 A:DQG601 4.5 9.3 1.0 C10 A:DQG601 4.5 17.9 0.5 SG A:CYS481 4.6 18.2 1.0 NE2 A:HIS483 4.6 8.7 1.0 CB A:HIS483 4.7 9.1 1.0 CD2 A:HIS483 4.7 10.1 1.0 C17 A:DQG601 4.7 39.4 1.0 CA A:PHE480 4.8 9.0 1.0 C27 A:DQG601 4.8 10.3 1.0 O A:HOH922 4.8 48.6 1.0 CL1 A:DQG601 4.8 13.2 0.5 C A:PHE480 4.9 11.1 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