Fluorine in PDB 6bgw: Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41)

Protein crystallography data

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41), PDB code: 6bgw 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) 32.88 / 1.64
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.577, 61.825, 46.758, 90.00, 92.13, 90.00
R / Rfree (%) 18.8 / 21.3

Other elements in 6bgw:

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41) 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)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41) (pdb code 6bgw). 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)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41), PDB code: 6bgw:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6bgw

Go back to Fluorine Binding Sites List in 6bgw
Fluorine binding site 1 out of 2 in the Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41)


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)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:47.7
occ:1.00
F22 A:DKS601 0.0 47.7 1.0
C21 A:DKS601 1.4 45.5 1.0
F23 A:DKS601 2.2 46.4 1.0
C20 A:DKS601 2.4 43.9 1.0
C24 A:DKS601 2.4 44.0 1.0
CE2 A:TRP470 2.9 30.1 1.0
NE1 A:TRP470 2.9 29.6 1.0
CZ2 A:TRP470 3.3 32.0 1.0
CD2 A:TRP470 3.5 28.6 1.0
CD1 A:TRP470 3.5 27.7 1.0
C19 A:DKS601 3.7 42.8 1.0
C25 A:DKS601 3.7 42.8 1.0
CG A:TRP470 3.8 26.2 1.0
CH2 A:TRP470 4.0 32.4 1.0
N18 A:DKS601 4.1 41.4 1.0
CE3 A:TRP470 4.2 29.7 1.0
CZ3 A:TRP470 4.5 31.4 1.0
OD2 A:ASP412 4.5 36.2 1.0
CG A:ASP412 4.6 34.9 1.0
OD1 A:ASP412 4.7 34.9 1.0
CB A:TRP470 4.9 22.3 1.0

Fluorine binding site 2 out of 2 in 6bgw

Go back to Fluorine Binding Sites List in 6bgw
Fluorine binding site 2 out of 2 in the Linked KDM5A Jmj Domain Bound to the Inhibitor 2-((2-Chlorophenyl)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41)


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)(2- (4,4-Difluoropiperidin-1-Yl)Ethoxy)Methyl)-1H-Pyrrolo[3,2-B]Pyridine- 7-Carboxylic Acid(Compound N41) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:46.4
occ:1.00
F23 A:DKS601 0.0 46.4 1.0
C21 A:DKS601 1.4 45.5 1.0
F22 A:DKS601 2.2 47.7 1.0
C20 A:DKS601 2.4 43.9 1.0
C24 A:DKS601 2.4 44.0 1.0
C19 A:DKS601 3.0 42.8 1.0
C25 A:DKS601 3.0 42.8 1.0
N18 A:DKS601 3.6 41.4 1.0
O A:HOH894 4.4 56.0 1.0
NE1 A:TRP470 4.5 29.6 1.0
O A:HOH785 4.7 28.0 1.0
C17 A:DKS601 4.7 38.2 1.0
CE2 A:TRP470 4.9 30.1 1.0
CD1 A:TRP470 4.9 27.7 1.0
O A:HOH878 5.0 51.7 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 12:45:33 2020

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