Iodine in PDB 7rxt: Crystal of BRD4(D1) with 2-[(3R)-3-{5-[2-(3,5-Dimethylphenoxy) Pyrimidin-4-Yl]-4-(4-Iodophenyl)-1H-Imidazol-1-Yl}Pyrrolidin-1- Yl]Ethan-1-Amine

The structure of Crystal of BRD4(D1) with 2-[(3R)-3-{5-[2-(3,5-Dimethylphenoxy) Pyrimidin-4-Yl]-4-(4-Iodophenyl)-1H-Imidazol-1-Yl}Pyrrolidin-1- Yl]Ethan-1-Amine, PDB code: 7rxt 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)	38.98 / 1.68
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	30.067, 41.663, 110.479, 90, 90, 90
R / Rfree (%)	20.1 / 23.8

The binding sites of Iodine atom in the Crystal of BRD4(D1) with 2-[(3R)-3-{5-[2-(3,5-Dimethylphenoxy) Pyrimidin-4-Yl]-4-(4-Iodophenyl)-1H-Imidazol-1-Yl}Pyrrolidin-1- Yl]Ethan-1-Amine (pdb code 7rxt). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total only one binding site of Iodine was determined in the Crystal of BRD4(D1) with 2-[(3R)-3-{5-[2-(3,5-Dimethylphenoxy) Pyrimidin-4-Yl]-4-(4-Iodophenyl)-1H-Imidazol-1-Yl}Pyrrolidin-1- Yl]Ethan-1-Amine, PDB code: 7rxt:

Iodine binding site 1 out of 1 in the Crystal of BRD4(D1) with 2-[(3R)-3-{5-[2-(3,5-Dimethylphenoxy) Pyrimidin-4-Yl]-4-(4-Iodophenyl)-1H-Imidazol-1-Yl}Pyrrolidin-1- Yl]Ethan-1-Amine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal of BRD4(D1) with 2-[(3R)-3-{5-[2-(3,5-Dimethylphenoxy) Pyrimidin-4-Yl]-4-(4-Iodophenyl)-1H-Imidazol-1-Yl}Pyrrolidin-1- Yl]Ethan-1-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:20.6 occ:0.74 I18 A:7ZK201 0.0 20.6 0.7 C17 A:7ZK201 2.1 19.2 1.0 C19 A:7ZK201 3.0 20.1 1.0 C16 A:7ZK201 3.1 17.8 1.0 O A:MET105 3.3 21.0 1.0 O A:HOH333 3.5 20.9 1.0 CG A:MET132 3.7 16.4 1.0 O A:MET132 3.9 19.4 1.0 OH A:TYR97 4.1 23.0 1.0 CD1 A:PHE83 4.2 16.4 1.0 C20 A:7ZK201 4.4 16.4 1.0 CG2 A:VAL87 4.4 24.8 1.0 C15 A:7ZK201 4.4 15.3 1.0 C A:MET105 4.5 18.0 1.0 C A:MET132 4.6 18.9 1.0 CA A:MET132 4.6 15.7 1.0 CB A:ASN135 4.6 20.1 1.0 CE1 A:PHE83 4.7 17.1 1.0 O A:HOH388 4.7 19.2 1.0 CB A:MET132 4.7 17.1 1.0 SD A:MET132 4.8 19.4 1.0 CA A:ASP106 4.8 17.3 1.0 C14 A:7ZK201 4.9 16.6 1.0 CB A:ASP106 4.9 18.4 1.0 N A:CYS136 5.0 18.5 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