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Fluorine in PDB 5ivf: Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol

Protein crystallography data

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol, PDB code: 5ivf 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 / 1.68
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.658, 62.289, 46.498, 90.00, 91.96, 90.00
R / Rfree (%) 16.9 / 20.2

Other elements in 5ivf:

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol (pdb code 5ivf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol, PDB code: 5ivf:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5ivf

Go back to Fluorine Binding Sites List in 5ivf
Fluorine binding site 1 out of 3 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol


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 N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:29.3
occ:1.00
F16 A:6EB601 0.0 29.3 1.0
C15 A:6EB601 1.3 30.3 1.0
F18 A:6EB601 2.1 33.6 1.0
F17 A:6EB601 2.1 30.5 1.0
C14 A:6EB601 2.3 29.0 1.0
C13 A:6EB601 2.8 25.8 1.0
NE2 A:GLN75 2.9 22.5 1.0
CD A:ARG73 3.1 55.4 1.0
O A:HOH852 3.5 33.7 1.0
NE A:ARG73 3.6 78.8 1.0
NH1 A:ARG73 3.8 30.1 1.0
CG A:ARG73 3.8 23.0 1.0
CD A:GLN75 3.8 17.9 1.0
CZ A:ARG73 4.0 71.1 1.0
O A:SER479 4.1 15.7 1.0
CD2 A:TYR409 4.1 14.5 1.0
O A:HOH704 4.1 41.7 1.0
CG A:GLN75 4.3 16.4 1.0
C12 A:6EB601 4.3 20.8 1.0
CB A:ALA411 4.6 13.9 1.0
O A:HOH782 4.7 43.2 1.0
OE1 A:GLN75 4.7 16.6 1.0
CB A:TYR409 4.8 17.0 1.0
CE2 A:TYR409 4.8 15.8 1.0
CG A:TYR409 4.9 12.8 1.0
O11 A:6EB601 4.9 17.6 1.0
NH2 A:ARG73 5.0 29.1 1.0

Fluorine binding site 2 out of 3 in 5ivf

Go back to Fluorine Binding Sites List in 5ivf
Fluorine binding site 2 out of 3 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol


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 N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:30.5
occ:1.00
F17 A:6EB601 0.0 30.5 1.0
C15 A:6EB601 1.3 30.3 1.0
F18 A:6EB601 2.1 33.6 1.0
F16 A:6EB601 2.1 29.3 1.0
C14 A:6EB601 2.3 29.0 1.0
NE2 A:GLN75 2.8 22.5 1.0
O A:HOH852 3.0 33.7 1.0
O A:HOH782 3.1 43.2 1.0
O A:HOH820 3.4 31.8 1.0
O A:SER479 3.4 15.7 1.0
C13 A:6EB601 3.5 25.8 1.0
CD A:GLN75 4.1 17.9 1.0
CA A:PHE480 4.4 10.1 1.0
C A:SER479 4.5 14.1 1.0
O A:HOH827 4.5 43.6 1.0
C12 A:6EB601 4.8 20.8 1.0
CG A:GLN75 4.8 16.4 1.0
O A:HOH704 4.8 41.7 1.0
N A:PHE480 4.9 8.6 1.0
CD A:ARG73 4.9 55.4 1.0
SG A:CYS481 5.0 33.0 0.5
NH1 A:ARG73 5.0 30.1 1.0

Fluorine binding site 3 out of 3 in 5ivf

Go back to Fluorine Binding Sites List in 5ivf
Fluorine binding site 3 out of 3 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol


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 N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:33.6
occ:1.00
F18 A:6EB601 0.0 33.6 1.0
C15 A:6EB601 1.3 30.3 1.0
F16 A:6EB601 2.1 29.3 1.0
F17 A:6EB601 2.1 30.5 1.0
C14 A:6EB601 2.3 29.0 1.0
NH1 A:ARG73 3.0 30.1 1.0
O A:HOH782 3.0 43.2 1.0
C13 A:6EB601 3.1 25.8 1.0
O A:HOH704 3.2 41.7 1.0
O A:HOH852 3.6 33.7 1.0
CZ A:ARG73 3.8 71.1 1.0
CD A:ARG73 3.8 55.4 1.0
O A:HOH820 4.0 31.8 1.0
NE A:ARG73 4.2 78.8 1.0
NE2 A:GLN75 4.4 22.5 1.0
C12 A:6EB601 4.5 20.8 1.0
O A:HOH756 4.5 26.4 1.0
NH2 A:ARG73 4.8 29.1 1.0

Reference:

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
Page generated: Tue Jul 15 04:12:49 2025

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