Fluorine in PDB 6bgx: Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)((4, 4-Difluorocyclohexyl)Methoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound N42)

Protein crystallography data

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)((4, 4-Difluorocyclohexyl)Methoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound N42), PDB code: 6bgx 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) 46.50 / 1.88
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.365, 61.850, 46.541, 90.00, 92.36, 90.00
R / Rfree (%) 19.9 / 23.6

Other elements in 6bgx:

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)((4, 4-Difluorocyclohexyl)Methoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound N42) also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)((4, 4-Difluorocyclohexyl)Methoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound N42) (pdb code 6bgx). 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)((4, 4-Difluorocyclohexyl)Methoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound N42), PDB code: 6bgx:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6bgx

Go back to Fluorine Binding Sites List in 6bgx
Fluorine binding site 1 out of 2 in the Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)((4, 4-Difluorocyclohexyl)Methoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound N42)


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)((4, 4-Difluorocyclohexyl)Methoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound N42) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:49.6
occ:1.00
F25 A:DKV601 0.0 49.6 1.0
C24 A:DKV601 1.4 47.8 1.0
F26 A:DKV601 2.2 50.9 1.0
O A:HOH732 2.3 52.0 1.0
C27 A:DKV601 2.4 45.6 1.0
C23 A:DKV601 2.4 45.5 1.0
OE1 A:GLU485 2.8 26.3 1.0
C28 A:DKV601 3.0 42.6 1.0
C22 A:DKV601 3.0 42.6 1.0
C21 A:DKV601 3.6 39.9 1.0
O A:HOH746 3.8 17.2 1.0
CD A:GLU485 3.8 25.5 1.0
CA A:GLU485 3.9 23.1 1.0
N A:ASP486 4.0 25.1 1.0
O A:ILE484 4.2 21.3 1.0
OD1 A:ASP486 4.3 32.0 1.0
CD2 A:HIS483 4.4 17.0 1.0
CB A:GLU485 4.4 24.0 1.0
C A:GLU485 4.5 23.8 1.0
O A:HOH737 4.5 39.5 1.0
OE2 A:GLU485 4.5 26.0 1.0
ND2 A:ASN585 4.6 26.3 1.0
CG A:ASP486 4.6 31.8 1.0
C20 A:DKV601 4.8 35.4 1.0
CG A:GLU485 4.8 24.3 1.0
N A:GLU485 4.8 21.9 1.0
C A:ILE484 4.8 20.7 1.0
OD2 A:ASP486 4.9 33.0 1.0
NE2 A:HIS483 4.9 16.6 1.0

Fluorine binding site 2 out of 2 in 6bgx

Go back to Fluorine Binding Sites List in 6bgx
Fluorine binding site 2 out of 2 in the Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)((4, 4-Difluorocyclohexyl)Methoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound N42)


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)((4, 4-Difluorocyclohexyl)Methoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine-7- Carboxylic Acid(Compound N42) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:50.9
occ:1.00
F26 A:DKV601 0.0 50.9 1.0
C24 A:DKV601 1.4 47.8 1.0
F25 A:DKV601 2.2 49.6 1.0
C23 A:DKV601 2.3 45.5 1.0
C27 A:DKV601 2.4 45.6 1.0
OD1 A:ASP486 2.6 32.0 1.0
CG A:ASP486 3.2 31.8 1.0
O A:HOH732 3.2 52.0 1.0
O A:HOH737 3.3 39.5 1.0
OD2 A:ASP486 3.5 33.0 1.0
C22 A:DKV601 3.7 42.6 1.0
C28 A:DKV601 3.7 42.6 1.0
N A:ASP486 3.9 25.1 1.0
O A:HOH827 4.0 40.2 1.0
C21 A:DKV601 4.2 39.9 1.0
O A:ILE484 4.3 21.3 1.0
CB A:ASP486 4.3 30.1 1.0
CA A:ASP486 4.6 27.1 1.0
C A:GLU485 4.6 23.8 1.0
CA A:GLU485 4.7 23.1 1.0
NE2 A:GLN535 4.7 31.8 1.0
OE1 A:GLU485 4.9 26.3 1.0

Reference:

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
Page generated: Sun Dec 13 12:45:35 2020

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