Atomistry » Fluorine » PDB 6b3e-6bkw » 6bgx
Atomistry »
  Fluorine »
    PDB 6b3e-6bkw »
      6bgx »

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: Tue Jul 15 10:06:45 2025

Last articles

Mg in 3SQX
Mg in 3SQS
Mg in 3SQW
Mg in 3SPT
Mg in 3SPR
Mg in 3SP5
Mg in 3SOP
Mg in 3SNN
Mg in 3SNL
Mg in 3SNI
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy