Chlorine in PDB 5iw0: Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid]

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid], PDB code: 5iw0 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)	32.97 / 1.63
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.320, 62.741, 46.609, 90.00, 91.93, 90.00
R / Rfree (%)	15.7 / 19.2

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid] 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 N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid] (pdb code 5iw0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid], PDB code: 5iw0:

Chlorine binding site 1 out of 1 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid]


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 N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid] within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:25.2 occ:1.00 CL1 A:6EP601 0.0 25.2 1.0 C17 A:6EP601 1.7 20.3 1.0 C19 A:6EP601 2.7 22.3 1.0 C16 A:6EP601 2.7 18.2 1.0 NE2 A:GLN75 3.2 19.9 1.0 CD A:ARG73 3.2 59.6 1.0 CG A:ARG73 3.6 24.9 1.0 O A:HOH701 3.6 32.5 1.0 CD2 A:TYR409 3.7 13.3 1.0 CB A:ALA411 3.8 17.6 1.0 CD A:GLN75 3.9 14.4 1.0 O4 A:AKG602 3.9 49.1 0.5 NE A:ARG73 4.0 50.9 1.0 C15 A:6EP601 4.0 18.6 1.0 C20 A:6EP601 4.0 21.4 1.0 CB A:TYR409 4.1 11.9 1.0 O A:SER479 4.1 14.2 1.0 O2 A:AKG602 4.2 43.4 0.5 CG A:TYR409 4.3 12.7 1.0 CG A:GLN75 4.4 14.6 1.0 O5 A:AKG602 4.4 36.6 0.5 C1 A:AKG602 4.5 42.3 0.5 C5 A:AKG602 4.5 47.1 0.5 C14 A:6EP601 4.5 17.7 1.0 CE2 A:TYR409 4.5 14.1 1.0 C2 A:AKG602 4.5 40.8 0.5 CZ A:ARG73 4.6 29.0 1.0 OE1 A:GLN75 4.6 15.9 1.0 NH1 A:ARG73 4.7 28.2 1.0 O A:HOH787 4.8 45.7 1.0 C3 A:AKG602 4.9 42.7 0.5 O3 A:AKG602 5.0 46.8 0.5

J.R.Horton, X.Liu, M.Gale, L.Wu, J.R.Shanks, X.Zhang, P.J.Webber, J.S.Bell, S.C.Kales, B.T.Mott, G.Rai, D.J.Jansen, M.J.Henderson, D.J.Urban, M.D.Hall, A.Simeonov, D.J.Maloney, M.A.Johns, H.Fu, A.Jadhav, P.M.Vertino, Q.Yan, X.Cheng. Structural Basis For KDM5A Histone Lysine Demethylase Inhibition By Diverse Compounds. Cell Chem Biol V. 23 769 2016.
ISSN: ESSN 2451-9456
PubMed: 27427228
DOI: 10.1016/J.CHEMBIOL.2016.06.006