Fluorine in PDB 5ivj: Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid]

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid], PDB code: 5ivj 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)	32.98 / 1.57
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.556, 62.516, 46.772, 90.00, 92.32, 90.00
R / Rfree (%)	15.9 / 18.9

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid] also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Fluorine atom in the Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid] (pdb code 5ivj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid], PDB code: 5ivj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid]


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 N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid] within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:22.1 occ:1.00 F28 A:6ED601 0.0 22.1 1.0 C27 A:6ED601 1.3 21.9 1.0 C29 A:6ED601 2.3 25.6 1.0 C26 A:6ED601 2.3 18.1 1.0 NE2 A:GLN75 3.2 15.6 1.0 CB A:ALA411 3.5 17.8 1.0 C25 A:6ED601 3.6 18.4 1.0 CD2 A:TYR409 3.6 12.3 1.0 C30 A:6ED601 3.6 26.5 1.0 CD A:ARG73 3.7 20.5 1.0 O A:SER479 3.8 12.1 1.0 O A:HOH872 3.8 24.7 1.0 NE A:ARG73 4.1 18.2 1.0 C24 A:6ED601 4.1 24.7 1.0 CE2 A:TYR409 4.1 12.3 1.0 NH1 A:ARG73 4.3 21.0 1.0 O A:HOH908 4.3 42.9 1.0 CZ A:ARG73 4.3 19.4 1.0 CD A:GLN75 4.3 11.5 1.0 CG A:ARG73 4.5 14.2 1.0 CG A:TYR409 4.5 10.9 1.0 O A:HOH890 4.5 32.5 1.0 O A:HOH864 4.6 33.6 1.0 CB A:TYR409 4.7 11.1 1.0 C11 A:6ED601 4.9 17.3 1.0 C A:SER479 5.0 13.0 1.0

Fluorine binding site 2 out of 5 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid]


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 N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid] within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:38.0 occ:0.50 F20 A:6ED601 0.0 38.0 0.5 C19 A:6ED601 1.4 36.9 0.5 F21 A:6ED601 2.2 37.3 0.5 C22 A:6ED601 2.4 34.7 0.5 C18 A:6ED601 2.4 36.7 0.5 NE2 A:GLN535 3.2 27.1 1.0 C17 A:6ED601 3.4 35.3 0.5 C23 A:6ED601 3.7 33.2 0.5 CB A:GLN535 4.0 24.2 1.0 O A:LEU532 4.1 29.9 1.0 N16 A:6ED601 4.1 32.5 0.5 CD2 A:LEU536 4.3 26.8 1.0 CD A:GLN535 4.4 30.6 1.0 O A:HOH920 4.7 46.0 1.0 O A:HOH781 4.7 31.2 1.0 CG A:GLN535 4.8 50.2 1.0 O A:GLN535 4.8 20.8 1.0 C A:GLN535 4.9 17.6 1.0 C A:LEU532 4.9 24.9 1.0

Fluorine binding site 3 out of 5 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid] within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:39.6 occ:0.50 F20 A:6ED601 0.0 39.6 0.5 C19 A:6ED601 1.4 39.0 0.5 F21 A:6ED601 2.2 39.5 0.5 C18 A:6ED601 2.4 37.9 0.5 C22 A:6ED601 2.4 38.3 0.5 CE2 A:TRP470 3.0 39.2 1.0 CD2 A:TRP470 3.1 36.1 1.0 CZ2 A:TRP470 3.1 46.2 1.0 CE3 A:TRP470 3.2 30.1 1.0 CH2 A:TRP470 3.3 31.0 1.0 CZ3 A:TRP470 3.3 30.0 1.0 C17 A:6ED601 3.7 37.4 0.5 C23 A:6ED601 3.7 37.9 0.5 NE1 A:TRP470 3.7 46.3 1.0 CG A:TRP470 3.8 28.4 1.0 CG A:ASP412 4.0 42.0 1.0 OD1 A:ASP412 4.1 44.1 1.0 N16 A:6ED601 4.1 36.9 0.5 CD1 A:TRP470 4.1 50.7 1.0 CB A:ASP412 4.2 29.6 1.0 C15 A:6ED601 4.3 34.1 0.5 OD2 A:ASP412 4.3 67.2 1.0 O A:HOH899 4.5 49.1 1.0 O A:HOH884 4.7 46.7 1.0 CB A:TRP470 4.8 16.6 1.0 CA A:ASP412 4.8 21.0 1.0

Fluorine binding site 4 out of 5 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid] within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:37.3 occ:0.50 F21 A:6ED601 0.0 37.3 0.5 C19 A:6ED601 1.4 36.9 0.5 F20 A:6ED601 2.2 38.0 0.5 C22 A:6ED601 2.3 34.7 0.5 C18 A:6ED601 2.3 36.7 0.5 O A:HOH920 2.9 46.0 1.0 C23 A:6ED601 3.0 33.2 0.5 CD2 A:LEU536 3.1 26.8 1.0 C17 A:6ED601 3.6 35.3 0.5 N16 A:6ED601 3.8 32.5 0.5 C14 A:6ED601 4.1 28.9 0.5 C14 A:6ED601 4.1 31.2 0.5 CG A:LEU536 4.4 20.2 1.0 O A:GLN535 4.5 20.8 1.0 C15 A:6ED601 4.5 29.8 0.5 C A:GLN535 4.8 17.6 1.0 N13 A:6ED601 4.8 27.4 1.0 CA A:LEU536 4.9 21.6 1.0 N A:LEU536 4.9 18.2 1.0 C17 A:6ED601 4.9 37.4 0.5 C30 A:6ED601 4.9 26.5 1.0 CB A:GLN535 5.0 24.2 1.0

Fluorine binding site 5 out of 5 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid]


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid] within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:39.5 occ:0.50 F21 A:6ED601 0.0 39.5 0.5 C19 A:6ED601 1.4 39.0 0.5 F20 A:6ED601 2.2 39.6 0.5 C22 A:6ED601 2.4 38.3 0.5 C18 A:6ED601 2.4 37.9 0.5 C17 A:6ED601 3.0 37.4 0.5 C23 A:6ED601 3.0 37.9 0.5 N16 A:6ED601 3.7 36.9 0.5 CE2 A:TRP470 3.9 39.2 1.0 CZ2 A:TRP470 4.0 46.2 1.0 NE1 A:TRP470 4.0 46.3 1.0 C15 A:6ED601 4.5 34.1 0.5 CD2 A:TRP470 4.5 36.1 1.0 CH2 A:TRP470 4.6 31.0 1.0 CD1 A:TRP470 4.7 50.7 1.0 CG A:TRP470 5.0 28.4 1.0

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