Bromine in PDB 7rxr: Crystal Structure of BRD4(D1) with 4-[4-(4-Bromophenyl)-1-(Piperidin- 4-Yl)-1H-Imidazol-5-Yl]-N-(3,5-Dimethylphenyl)Pyrimidin-2-Amine

The structure of Crystal Structure of BRD4(D1) with 4-[4-(4-Bromophenyl)-1-(Piperidin- 4-Yl)-1H-Imidazol-5-Yl]-N-(3,5-Dimethylphenyl)Pyrimidin-2-Amine, PDB code: 7rxr was solved by H.Cui, J.A.Johnson, 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)	55.72 / 1.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.106, 59.345, 111.443, 90, 90, 90
R / Rfree (%)	15 / 18.6

The binding sites of Bromine atom in the Crystal Structure of BRD4(D1) with 4-[4-(4-Bromophenyl)-1-(Piperidin- 4-Yl)-1H-Imidazol-5-Yl]-N-(3,5-Dimethylphenyl)Pyrimidin-2-Amine (pdb code 7rxr). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of BRD4(D1) with 4-[4-(4-Bromophenyl)-1-(Piperidin- 4-Yl)-1H-Imidazol-5-Yl]-N-(3,5-Dimethylphenyl)Pyrimidin-2-Amine, PDB code: 7rxr:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of BRD4(D1) with 4-[4-(4-Bromophenyl)-1-(Piperidin- 4-Yl)-1H-Imidazol-5-Yl]-N-(3,5-Dimethylphenyl)Pyrimidin-2-Amine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of BRD4(D1) with 4-[4-(4-Bromophenyl)-1-(Piperidin- 4-Yl)-1H-Imidazol-5-Yl]-N-(3,5-Dimethylphenyl)Pyrimidin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br202 b:28.1 occ:0.96 BR15 A:7ZB202 0.0 28.1 1.0 C14 A:7ZB202 1.9 21.6 1.0 C13 A:7ZB202 2.8 20.4 1.0 C16 A:7ZB202 2.9 19.6 1.0 O A:MET105 3.3 16.8 1.0 O A:HOH342 3.5 18.8 1.0 CG A:MET132 3.7 16.1 1.0 O A:MET132 3.9 15.5 1.0 CD1 A:PHE83 4.1 16.3 1.0 C12 A:7ZB202 4.1 19.7 1.0 C17 A:7ZB202 4.2 17.4 1.0 CG2 A:VAL87 4.2 17.5 1.0 OH A:TYR97 4.2 19.9 1.0 C A:MET105 4.5 15.0 1.0 CE1 A:PHE83 4.5 16.9 1.0 CB A:MET132 4.6 18.6 1.0 C A:MET132 4.6 14.8 1.0 CA A:MET132 4.6 16.4 1.0 C11 A:7ZB202 4.6 17.3 1.0 SD A:MET132 4.8 16.7 1.0 CB A:ASN135 4.8 19.2 1.0 CA A:ASP106 4.9 14.7 1.0 CB A:CYS136 5.0 17.1 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of BRD4(D1) with 4-[4-(4-Bromophenyl)-1-(Piperidin- 4-Yl)-1H-Imidazol-5-Yl]-N-(3,5-Dimethylphenyl)Pyrimidin-2-Amine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of BRD4(D1) with 4-[4-(4-Bromophenyl)-1-(Piperidin- 4-Yl)-1H-Imidazol-5-Yl]-N-(3,5-Dimethylphenyl)Pyrimidin-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Br204 b:22.4 occ:0.86 BR15 B:7ZB204 0.0 22.4 0.9 C14 B:7ZB204 1.9 18.9 1.0 C13 B:7ZB204 2.9 18.1 1.0 C16 B:7ZB204 2.9 18.1 1.0 O B:MET105 3.2 16.6 1.0 O B:HOH340 3.6 16.7 1.0 CG B:MET132 3.7 18.0 1.0 O B:MET132 4.0 14.8 1.0 CD1 B:PHE83 4.1 16.0 1.0 C12 B:7ZB204 4.1 18.5 1.0 C17 B:7ZB204 4.1 17.0 1.0 OH B:TYR97 4.2 18.4 1.0 CG2 B:VAL87 4.2 18.4 1.0 C B:MET105 4.4 16.0 1.0 CE1 B:PHE83 4.6 16.6 1.0 CA B:MET132 4.6 16.1 1.0 C B:MET132 4.6 16.9 1.0 CB B:MET132 4.6 17.0 1.0 C11 B:7ZB204 4.6 16.6 1.0 SD B:MET132 4.7 17.6 1.0 CA B:ASP106 4.7 15.8 1.0 CB B:ASN135 4.8 17.0 1.0 CB B:ASP106 4.8 17.8 1.0

H.Cui, A.Divakaran, Z.J.Hoell, M.O.Ellingson, C.R.Scholtz, H.Zahid, J.A.Johnson, E.C.Griffith, C.T.Gee, A.L.Lee, S.Khanal, K.Shi, H.Aihara, V.H.Shah, R.E.Lee, D.A.Harki, W.C.K.Pomerantz. A Structure-Based Design Approach For Generating High Affinity BRD4 D1-Selective Chemical Probes. J.Med.Chem. V. 65 2342 2022.
ISSN: ISSN 0022-2623
PubMed: 35007061
DOI: 10.1021/ACS.JMEDCHEM.1C01779