Fluorine in PDB 6bgw: Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41)

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41), PDB code: 6bgw 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)	32.88 / 1.64
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.577, 61.825, 46.758, 90.00, 92.13, 90.00
R / Rfree (%)	18.8 / 21.3

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41) also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41) (pdb code 6bgw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41), PDB code: 6bgw:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41) within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:47.7 occ:1.00 F22 A:DKS601 0.0 47.7 1.0 C21 A:DKS601 1.4 45.5 1.0 F23 A:DKS601 2.2 46.4 1.0 C20 A:DKS601 2.4 43.9 1.0 C24 A:DKS601 2.4 44.0 1.0 CE2 A:TRP470 2.9 30.1 1.0 NE1 A:TRP470 2.9 29.6 1.0 CZ2 A:TRP470 3.3 32.0 1.0 CD2 A:TRP470 3.5 28.6 1.0 CD1 A:TRP470 3.5 27.7 1.0 C19 A:DKS601 3.7 42.8 1.0 C25 A:DKS601 3.7 42.8 1.0 CG A:TRP470 3.8 26.2 1.0 CH2 A:TRP470 4.0 32.4 1.0 N18 A:DKS601 4.1 41.4 1.0 CE3 A:TRP470 4.2 29.7 1.0 CZ3 A:TRP470 4.5 31.4 1.0 OD2 A:ASP412 4.5 36.2 1.0 CG A:ASP412 4.6 34.9 1.0 OD1 A:ASP412 4.7 34.9 1.0 CB A:TRP470 4.9 22.3 1.0

Fluorine binding site 2 out of 2 in the Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41) within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:46.4 occ:1.00 F23 A:DKS601 0.0 46.4 1.0 C21 A:DKS601 1.4 45.5 1.0 F22 A:DKS601 2.2 47.7 1.0 C20 A:DKS601 2.4 43.9 1.0 C24 A:DKS601 2.4 44.0 1.0 C19 A:DKS601 3.0 42.8 1.0 C25 A:DKS601 3.0 42.8 1.0 N18 A:DKS601 3.6 41.4 1.0 O A:HOH894 4.4 56.0 1.0 NE1 A:TRP470 4.5 29.6 1.0 O A:HOH785 4.7 28.0 1.0 C17 A:DKS601 4.7 38.2 1.0 CE2 A:TRP470 4.9 30.1 1.0 CD1 A:TRP470 4.9 27.7 1.0 O A:HOH878 5.0 51.7 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