Fluorine in PDB 6wgx: Cocrystal of BRD4(D1) with A Selective Inhibitor

The structure of Cocrystal of BRD4(D1) with A Selective Inhibitor, PDB code: 6wgx was solved by J.A.Johnson, H.Cui, K.Shi, H.Aihara, W.C.K.Pomerantz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.40 / 1.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.909, 59.198, 112.604, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 18.1

The binding sites of Fluorine atom in the Cocrystal of BRD4(D1) with A Selective Inhibitor (pdb code 6wgx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Cocrystal of BRD4(D1) with A Selective Inhibitor, PDB code: 6wgx:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Cocrystal of BRD4(D1) with A Selective Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cocrystal of BRD4(D1) with A Selective Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:23.6 occ:1.00 F1 A:U0D202 0.0 23.6 1.0 C29 A:U0D202 1.1 23.0 1.0 F2 A:U0D202 1.9 23.2 1.0 F3 A:U0D202 1.9 22.8 1.0 C3 A:U0D202 2.1 19.6 1.0 C2 A:U0D202 2.7 20.4 1.0 HG3 A:MET132 3.0 20.7 1.0 HD1 A:PHE83 3.1 21.5 1.0 C4 A:U0D202 3.4 19.7 1.0 O A:MET105 3.5 18.3 1.0 HG2 A:MET132 3.6 20.7 1.0 HA A:PHE83 3.6 19.6 1.0 HG23 A:VAL87 3.6 23.9 1.0 CG A:MET132 3.7 17.3 1.0 HA A:ASP106 3.8 19.6 1.0 CD1 A:PHE83 3.8 17.9 1.0 HB3 A:ASP106 3.9 20.2 1.0 HG21 A:VAL87 4.0 23.9 1.0 C1 A:U0D202 4.0 20.2 1.0 O A:HOH364 4.1 20.7 1.0 CG2 A:VAL87 4.1 19.9 1.0 HG22 A:VAL87 4.2 23.9 1.0 HE1 A:PHE83 4.3 23.0 1.0 HB2 A:ASP106 4.4 20.2 1.0 HB3 A:PHE83 4.4 19.7 1.0 SD A:MET132 4.4 17.8 1.0 CB A:ASP106 4.5 16.8 1.0 CE1 A:PHE83 4.5 19.1 1.0 CA A:PHE83 4.5 16.3 1.0 C5 A:U0D202 4.5 20.4 1.0 HB2 A:CYS136 4.5 24.3 1.0 CA A:ASP106 4.5 16.4 1.0 O A:PRO82 4.5 18.7 1.0 O A:MET132 4.5 16.4 1.0 C A:MET105 4.6 17.1 1.0 HA A:MET132 4.6 18.6 1.0 CG A:PHE83 4.7 16.8 1.0 CB A:PHE83 4.8 16.4 1.0 HH A:TYR97 4.8 22.7 1.0 C6 A:U0D202 4.8 21.1 1.0 OH A:TYR97 4.8 18.9 1.0 HB2 A:ASN135 4.9 22.4 1.0 CB A:MET132 4.9 15.0 1.0

Fluorine binding site 2 out of 6 in the Cocrystal of BRD4(D1) with A Selective Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cocrystal of BRD4(D1) with A Selective Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:23.2 occ:1.00 F2 A:U0D202 0.0 23.2 1.0 C29 A:U0D202 1.2 23.0 1.0 F1 A:U0D202 1.9 23.6 1.0 F3 A:U0D202 1.9 22.8 1.0 C3 A:U0D202 2.1 19.6 1.0 HD1 A:PHE83 2.6 21.5 1.0 HG2 A:MET132 2.7 20.7 1.0 HB2 A:CYS136 2.8 24.3 1.0 C2 A:U0D202 2.9 20.4 1.0 HG3 A:MET132 3.0 20.7 1.0 HE1 A:PHE83 3.1 23.0 1.0 O A:MET132 3.1 16.4 1.0 C4 A:U0D202 3.1 19.7 1.0 CG A:MET132 3.3 17.3 1.0 CD1 A:PHE83 3.3 17.9 1.0 CE1 A:PHE83 3.6 19.1 1.0 H A:CYS136 3.8 22.6 1.0 CB A:CYS136 3.8 20.3 1.0 C A:MET132 3.8 16.0 1.0 HA A:MET132 4.0 18.6 1.0 HB2 A:ASN135 4.1 22.4 1.0 C1 A:U0D202 4.2 20.2 1.0 HB3 A:CYS136 4.2 24.3 1.0 N A:CYS136 4.3 18.8 1.0 C5 A:U0D202 4.3 20.4 1.0 CA A:MET132 4.3 15.5 1.0 O A:MET105 4.4 18.3 1.0 CB A:MET132 4.4 15.0 1.0 HA A:PHE133 4.4 21.3 1.0 SD A:MET132 4.4 17.8 1.0 CA A:CYS136 4.5 19.9 1.0 HA A:CYS136 4.5 23.9 1.0 HA A:PHE83 4.6 19.6 1.0 CG A:PHE83 4.6 16.8 1.0 HE3 A:MET132 4.6 23.0 1.0 HG A:CYS136 4.7 25.9 1.0 HB3 A:PHE83 4.7 19.7 1.0 SG A:CYS136 4.7 21.6 1.0 N A:PHE133 4.8 16.8 1.0 C6 A:U0D202 4.8 21.1 1.0 HA A:ASP106 4.8 19.6 1.0 CB A:ASN135 4.9 18.7 1.0 HB3 A:ASN135 4.9 22.4 1.0 CZ A:PHE83 4.9 18.9 1.0 O A:HOH364 4.9 20.7 1.0 HB3 A:MET132 5.0 18.0 1.0 HB2 A:MET132 5.0 18.0 1.0

Fluorine binding site 3 out of 6 in the Cocrystal of BRD4(D1) with A Selective Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cocrystal of BRD4(D1) with A Selective Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:22.8 occ:1.00 F3 A:U0D202 0.0 22.8 1.0 C29 A:U0D202 1.2 23.0 1.0 F1 A:U0D202 1.9 23.6 1.0 F2 A:U0D202 1.9 23.2 1.0 C3 A:U0D202 2.2 19.6 1.0 C4 A:U0D202 2.7 19.7 1.0 HB2 A:ASN135 3.1 22.4 1.0 O A:HOH364 3.1 20.7 1.0 HG3 A:MET132 3.3 20.7 1.0 HH A:TYR97 3.4 22.7 1.0 C2 A:U0D202 3.4 20.4 1.0 OH A:TYR97 3.4 18.9 1.0 O A:MET105 3.4 18.3 1.0 O A:MET132 3.5 16.4 1.0 HB3 A:ASN135 3.6 22.4 1.0 HD22 A:ASN135 3.7 23.1 1.0 HA A:MET132 3.8 18.6 1.0 CB A:ASN135 3.8 18.7 1.0 HB2 A:CYS136 3.8 24.3 1.0 HG23 A:VAL87 3.8 23.9 1.0 HG2 A:MET132 3.8 20.7 1.0 HG22 A:VAL87 3.9 23.9 1.0 H A:CYS136 3.9 22.6 1.0 CG A:MET132 4.0 17.3 1.0 C5 A:U0D202 4.0 20.4 1.0 N A:CYS136 4.2 18.8 1.0 CG2 A:VAL87 4.3 19.9 1.0 C A:MET132 4.3 16.0 1.0 HD1 A:PHE83 4.3 21.5 1.0 H A:MET105 4.4 20.1 1.0 CA A:MET132 4.4 15.5 1.0 ND2 A:ASN135 4.5 19.2 1.0 HG21 A:VAL87 4.5 23.9 1.0 HA A:CYS136 4.5 23.9 1.0 C1 A:U0D202 4.6 20.2 1.0 CB A:CYS136 4.7 20.3 1.0 C A:MET105 4.7 17.1 1.0 CZ A:TYR97 4.7 19.3 1.0 C A:ASN135 4.7 18.1 1.0 CG A:ASN135 4.7 19.1 1.0 CA A:CYS136 4.7 19.9 1.0 CB A:MET132 4.8 15.0 1.0 CA A:ASN135 4.8 18.6 1.0 HE1 A:PHE83 4.8 23.0 1.0 HA A:ASP106 4.8 19.6 1.0 C6 A:U0D202 4.9 21.1 1.0 HB3 A:ASP106 5.0 20.2 1.0

Fluorine binding site 4 out of 6 in the Cocrystal of BRD4(D1) with A Selective Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cocrystal of BRD4(D1) with A Selective Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:22.6 occ:1.00 F1 B:U0D202 0.0 22.6 1.0 C29 B:U0D202 1.2 20.8 1.0 F2 B:U0D202 1.9 20.4 1.0 F3 B:U0D202 2.0 20.6 1.0 C3 B:U0D202 2.2 16.8 1.0 C2 B:U0D202 2.7 15.9 1.0 HG3 B:MET132 2.9 19.9 1.0 HD1 B:PHE83 3.1 21.5 1.0 C4 B:U0D202 3.4 16.8 1.0 O B:MET105 3.4 18.9 1.0 HG2 B:MET132 3.5 19.9 1.0 HG23 B:VAL87 3.6 23.3 1.0 HA B:PHE83 3.6 18.7 1.0 CG B:MET132 3.6 16.6 1.0 HA B:ASP106 3.7 19.8 1.0 HB3 B:ASP106 3.9 21.7 1.0 CD1 B:PHE83 3.9 17.9 1.0 HG21 B:VAL87 4.0 23.3 1.0 C1 B:U0D202 4.0 16.4 1.0 CG2 B:VAL87 4.1 19.4 1.0 HG22 B:VAL87 4.1 23.3 1.0 O B:HOH344 4.1 18.4 1.0 HB2 B:ASP106 4.3 21.7 1.0 HE1 B:PHE83 4.3 21.1 1.0 CB B:ASP106 4.4 18.1 1.0 HB3 B:PHE83 4.4 19.4 1.0 CA B:ASP106 4.4 16.5 1.0 SD B:MET132 4.4 17.9 1.0 C5 B:U0D202 4.5 17.3 1.0 C B:MET105 4.5 17.0 1.0 CE1 B:PHE83 4.5 17.6 1.0 CA B:PHE83 4.5 15.6 1.0 HA B:MET132 4.5 18.4 1.0 HB2 B:CYS136 4.6 19.6 1.0 O B:MET132 4.6 15.2 1.0 O B:PRO82 4.6 18.0 1.0 OH B:TYR97 4.7 17.2 1.0 CG B:PHE83 4.8 17.3 1.0 CB B:PHE83 4.8 16.1 1.0 HH B:TYR97 4.8 20.7 1.0 CB B:MET132 4.8 16.1 1.0 C6 B:U0D202 4.8 16.2 1.0 HB2 B:ASN135 4.9 18.4 1.0 N B:ASP106 5.0 16.3 1.0

Fluorine binding site 5 out of 6 in the Cocrystal of BRD4(D1) with A Selective Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cocrystal of BRD4(D1) with A Selective Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:20.4 occ:1.00 F2 B:U0D202 0.0 20.4 1.0 C29 B:U0D202 1.2 20.8 1.0 F1 B:U0D202 1.9 22.6 1.0 F3 B:U0D202 2.0 20.6 1.0 C3 B:U0D202 2.1 16.8 1.0 HD1 B:PHE83 2.6 21.5 1.0 HG2 B:MET132 2.7 19.9 1.0 HB2 B:CYS136 2.8 19.6 1.0 C2 B:U0D202 2.9 15.9 1.0 HG3 B:MET132 3.0 19.9 1.0 HE1 B:PHE83 3.0 21.1 1.0 C4 B:U0D202 3.1 16.8 1.0 O B:MET132 3.1 15.2 1.0 CG B:MET132 3.3 16.6 1.0 CD1 B:PHE83 3.3 17.9 1.0 CE1 B:PHE83 3.5 17.6 1.0 H B:CYS136 3.8 17.8 1.0 CB B:CYS136 3.8 16.4 1.0 C B:MET132 3.8 15.0 1.0 HA B:MET132 4.0 18.4 1.0 HB2 B:ASN135 4.1 18.4 1.0 C1 B:U0D202 4.2 16.4 1.0 N B:CYS136 4.2 14.8 1.0 HB3 B:CYS136 4.2 19.6 1.0 C5 B:U0D202 4.3 17.3 1.0 CA B:MET132 4.3 15.3 1.0 CB B:MET132 4.4 16.1 1.0 HA B:CYS136 4.4 19.1 1.0 HA B:PHE133 4.4 17.9 1.0 CA B:CYS136 4.4 16.0 1.0 SD B:MET132 4.4 17.9 1.0 O B:MET105 4.4 18.9 1.0 HE3 B:MET132 4.5 22.4 1.0 CG B:PHE83 4.6 17.3 1.0 HA B:PHE83 4.6 18.7 1.0 HG B:CYS136 4.6 21.6 1.0 HB3 B:PHE83 4.7 19.4 1.0 SG B:CYS136 4.7 18.0 1.0 N B:PHE133 4.7 15.7 1.0 HA B:ASP106 4.8 19.8 1.0 C6 B:U0D202 4.8 16.2 1.0 HB3 B:ASN135 4.8 18.4 1.0 CZ B:PHE83 4.9 16.6 1.0 CB B:ASN135 4.9 15.4 1.0 HB3 B:MET132 4.9 19.3 1.0 HB2 B:MET132 5.0 19.3 1.0

Fluorine binding site 6 out of 6 in the Cocrystal of BRD4(D1) with A Selective Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cocrystal of BRD4(D1) with A Selective Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:20.6 occ:1.00 F3 B:U0D202 0.0 20.6 1.0 C29 B:U0D202 1.2 20.8 1.0 F2 B:U0D202 2.0 20.4 1.0 F1 B:U0D202 2.0 22.6 1.0 C3 B:U0D202 2.2 16.8 1.0 C4 B:U0D202 2.7 16.8 1.0 HB2 B:ASN135 3.0 18.4 1.0 O B:HOH344 3.2 18.4 1.0 OH B:TYR97 3.3 17.2 1.0 HG3 B:MET132 3.4 19.9 1.0 HB3 B:ASN135 3.4 18.4 1.0 HH B:TYR97 3.4 20.7 1.0 O B:MET132 3.4 15.2 1.0 O B:MET105 3.4 18.9 1.0 C2 B:U0D202 3.5 15.9 1.0 HD22 B:ASN135 3.6 20.6 1.0 CB B:ASN135 3.6 15.4 1.0 HA B:MET132 3.7 18.4 1.0 HG2 B:MET132 3.8 19.9 1.0 HB2 B:CYS136 3.8 19.6 1.0 H B:CYS136 3.8 17.8 1.0 HG22 B:VAL87 4.0 23.3 1.0 HG23 B:VAL87 4.0 23.3 1.0 CG B:MET132 4.0 16.6 1.0 C5 B:U0D202 4.0 17.3 1.0 N B:CYS136 4.1 14.8 1.0 C B:MET132 4.2 15.0 1.0 CA B:MET132 4.3 15.3 1.0 ND2 B:ASN135 4.4 17.2 1.0 CG2 B:VAL87 4.4 19.4 1.0 HA B:CYS136 4.4 19.1 1.0 HD1 B:PHE83 4.4 21.5 1.0 H B:MET105 4.4 19.9 1.0 C B:ASN135 4.5 15.0 1.0 CG B:ASN135 4.6 16.4 1.0 CZ B:TYR97 4.6 17.5 1.0 CA B:CYS136 4.6 16.0 1.0 HG21 B:VAL87 4.6 23.3 1.0 CB B:CYS136 4.6 16.4 1.0 C1 B:U0D202 4.6 16.4 1.0 C B:MET105 4.7 17.0 1.0 CA B:ASN135 4.7 15.0 1.0 CB B:MET132 4.8 16.1 1.0 HA B:ASP106 4.8 19.8 1.0 HE1 B:PHE83 4.9 21.1 1.0 C6 B:U0D202 4.9 16.2 1.0

H.Cui, A.Divakaran, A.K.Pandey, J.A.Johnson, H.Zahid, Z.J.Hoell, M.O.Ellingson, K.Shi, H.Aihara, D.A.Harki, W.C.K.Pomerantz. Selective N-Terminal Bet Bromodomain Inhibitors By Targeting Non-Conserved Residues and Structured Water Displacement*. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32975004
DOI: 10.1002/ANIE.202008625