Fluorine in PDB 6mh7: Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Skt-68, A 1,4,5-Trisubstituted Imidazole Analogue

Protein crystallography data

The structure of Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Skt-68, A 1,4,5-Trisubstituted Imidazole Analogue, PDB code: 6mh7 was solved by J.-Y.Zhu, E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.11 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.750, 59.370, 111.820, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Skt-68, A 1,4,5-Trisubstituted Imidazole Analogue (pdb code 6mh7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Skt-68, A 1,4,5-Trisubstituted Imidazole Analogue, PDB code: 6mh7:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6mh7

Go back to Fluorine Binding Sites List in 6mh7
Fluorine binding site 1 out of 2 in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Skt-68, A 1,4,5-Trisubstituted Imidazole Analogue


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Skt-68, A 1,4,5-Trisubstituted Imidazole Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:18.1
occ:1.00
F01 A:JQY201 0.0 18.1 1.0
C02 A:JQY201 1.3 15.1 1.0
C05 A:JQY201 2.3 13.3 1.0
C03 A:JQY201 2.4 14.4 1.0
H051 A:JQY201 2.6 16.0 1.0
H031 A:JQY201 2.6 17.3 1.0
O A:HOH307 2.8 21.6 1.0
HD1 A:PHE83 2.9 17.0 1.0
HG3 A:MET132 3.0 16.6 1.0
HG2 A:MET132 3.3 16.6 1.0
HE1 A:PHE83 3.4 19.1 1.0
HB2 A:CYS136 3.5 14.7 1.0
CD1 A:PHE83 3.6 14.1 1.0
C06 A:JQY201 3.6 12.6 1.0
CG A:MET132 3.6 13.9 1.0
C04 A:JQY201 3.6 14.1 1.0
O A:MET132 3.7 12.1 1.0
CE1 A:PHE83 3.8 15.9 1.0
O A:MET105 4.0 14.0 1.0
C07 A:JQY201 4.1 13.3 1.0
HG23 A:VAL87 4.1 17.3 1.0
HG21 A:VAL87 4.2 17.3 1.0
HB2 A:ASN135 4.2 16.8 1.0
HA A:PHE83 4.3 12.4 1.0
HA A:MET132 4.3 16.9 1.0
O A:HOH329 4.3 13.6 1.0
H A:CYS136 4.4 13.5 1.0
H061 A:JQY201 4.4 15.1 1.0
HG22 A:VAL87 4.4 17.3 1.0
OH A:TYR97 4.4 15.0 1.0
H041 A:JQY201 4.4 16.9 1.0
HH A:TYR97 4.4 18.0 1.0
CB A:CYS136 4.5 12.2 1.0
CG2 A:VAL87 4.5 14.4 1.0
C A:MET132 4.5 14.0 1.0
HA A:ASP106 4.6 11.8 1.0
SD A:MET132 4.7 13.1 1.0
HA A:CYS136 4.7 11.7 1.0
CG A:PHE83 4.7 9.8 1.0
N A:CYS136 4.7 11.2 1.0
CA A:MET132 4.7 14.1 1.0
CB A:MET132 4.8 11.7 1.0
CA A:CYS136 4.9 9.8 1.0
HB3 A:ASN135 4.9 16.8 1.0
HB3 A:PHE83 4.9 12.2 1.0
HD21 A:ASN135 4.9 16.3 1.0

Fluorine binding site 2 out of 2 in 6mh7

Go back to Fluorine Binding Sites List in 6mh7
Fluorine binding site 2 out of 2 in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Skt-68, A 1,4,5-Trisubstituted Imidazole Analogue


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Skt-68, A 1,4,5-Trisubstituted Imidazole Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:21.7
occ:1.00
F01 B:JQY201 0.0 21.7 1.0
C02 B:JQY201 1.3 18.1 1.0
C05 B:JQY201 2.3 17.0 1.0
C03 B:JQY201 2.4 16.6 1.0
H051 B:JQY201 2.6 20.4 1.0
H031 B:JQY201 2.6 20.0 1.0
O B:HOH326 2.9 19.7 1.0
HD1 B:PHE83 2.9 15.5 1.0
HG3 B:MET132 3.2 17.7 1.0
HG2 B:MET132 3.3 17.7 1.0
HB2 B:CYS136 3.3 14.4 1.0
HE1 B:PHE83 3.3 19.5 1.0
CD1 B:PHE83 3.5 12.9 1.0
O B:MET132 3.5 15.1 1.0
C06 B:JQY201 3.6 16.6 1.0
C04 B:JQY201 3.6 18.3 1.0
CG B:MET132 3.7 14.8 1.0
CE1 B:PHE83 3.7 16.2 1.0
C07 B:JQY201 4.1 17.7 1.0
HG23 B:VAL87 4.2 18.4 1.0
HA B:PHE83 4.2 15.4 1.0
HG21 B:VAL87 4.2 18.4 1.0
O B:MET105 4.2 13.6 1.0
HB2 B:ASN135 4.3 14.8 1.0
CB B:CYS136 4.3 12.1 1.0
HH B:TYR97 4.3 22.1 1.0
H B:CYS136 4.4 15.4 1.0
C B:MET132 4.4 13.7 1.0
HA B:MET132 4.4 10.9 1.0
H061 B:JQY201 4.4 19.9 1.0
H041 B:JQY201 4.4 21.9 1.0
HG22 B:VAL87 4.5 18.4 1.0
CG2 B:VAL87 4.5 15.3 1.0
O B:HOH321 4.6 16.8 1.0
OH B:TYR97 4.6 18.5 1.0
CG B:PHE83 4.6 10.2 1.0
HA B:CYS136 4.7 19.5 1.0
N B:CYS136 4.7 12.8 1.0
CA B:MET132 4.7 9.1 1.0
HB3 B:CYS136 4.8 14.4 1.0
CB B:MET132 4.8 14.2 1.0
SD B:MET132 4.8 13.2 1.0
CA B:CYS136 4.8 16.3 1.0
HB3 B:PHE83 4.9 15.2 1.0
HG B:CYS136 4.9 17.6 1.0
HA B:ASP106 4.9 18.1 1.0
CZ B:PHE83 4.9 16.9 1.0

Reference:

A.Divakaran, S.K.Talluri, A.M.Ayoub, N.K.Mishra, H.Cui, J.C.Widen, N.Berndt, J.Y.Zhu, A.S.Carlson, J.J.Topczewski, E.K.Schonbrunn, D.A.Harki, W.C.K.Pomerantz. Molecular Basis For the N-Terminal Bromodomain-and-Extra-Terminal-Family Selectivity of A Dual Kinase-Bromodomain Inhibitor. J.Med.Chem. V. 61 9316 2018.
ISSN: ISSN 0022-2623
PubMed: 30253095
DOI: 10.1021/ACS.JMEDCHEM.8B01248
Page generated: Sun Dec 13 12:58:49 2020

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