Chlorine in PDB 7r9c: Cocrystal of BRD4(D1) with N,N-Dimethyl-2-[(3R)-3-(5-{2-[2-Methyl-5- (Propan-2-Yl)Phenoxy]Pyrimidin-4-Yl}-4-[4-(Trifluoromethyl)Phenyl]- 1H-Imidazol-1-Yl)Pyrrolidin-1-Yl]Ethan-1-Amine

The structure of Cocrystal of BRD4(D1) with N,N-Dimethyl-2-[(3R)-3-(5-{2-[2-Methyl-5- (Propan-2-Yl)Phenoxy]Pyrimidin-4-Yl}-4-[4-(Trifluoromethyl)Phenyl]- 1H-Imidazol-1-Yl)Pyrrolidin-1-Yl]Ethan-1-Amine, PDB code: 7r9c was solved by 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)	35.57 / 1.50
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	29.948, 37.553, 110.959, 90, 90, 90
R / Rfree (%)	16.8 / 21.6

The structure of Cocrystal of BRD4(D1) with N,N-Dimethyl-2-[(3R)-3-(5-{2-[2-Methyl-5- (Propan-2-Yl)Phenoxy]Pyrimidin-4-Yl}-4-[4-(Trifluoromethyl)Phenyl]- 1H-Imidazol-1-Yl)Pyrrolidin-1-Yl]Ethan-1-Amine also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Chlorine atom in the Cocrystal of BRD4(D1) with N,N-Dimethyl-2-[(3R)-3-(5-{2-[2-Methyl-5- (Propan-2-Yl)Phenoxy]Pyrimidin-4-Yl}-4-[4-(Trifluoromethyl)Phenyl]- 1H-Imidazol-1-Yl)Pyrrolidin-1-Yl]Ethan-1-Amine (pdb code 7r9c). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Cocrystal of BRD4(D1) with N,N-Dimethyl-2-[(3R)-3-(5-{2-[2-Methyl-5- (Propan-2-Yl)Phenoxy]Pyrimidin-4-Yl}-4-[4-(Trifluoromethyl)Phenyl]- 1H-Imidazol-1-Yl)Pyrrolidin-1-Yl]Ethan-1-Amine, PDB code: 7r9c:

Chlorine binding site 1 out of 1 in the Cocrystal of BRD4(D1) with N,N-Dimethyl-2-[(3R)-3-(5-{2-[2-Methyl-5- (Propan-2-Yl)Phenoxy]Pyrimidin-4-Yl}-4-[4-(Trifluoromethyl)Phenyl]- 1H-Imidazol-1-Yl)Pyrrolidin-1-Yl]Ethan-1-Amine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cocrystal of BRD4(D1) with N,N-Dimethyl-2-[(3R)-3-(5-{2-[2-Methyl-5- (Propan-2-Yl)Phenoxy]Pyrimidin-4-Yl}-4-[4-(Trifluoromethyl)Phenyl]- 1H-Imidazol-1-Yl)Pyrrolidin-1-Yl]Ethan-1-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl207 b:64.1 occ:1.00 HE1 A:TRP75 2.2 29.3 1.0 NE1 A:TRP75 3.0 24.4 1.0 H22 A:EDO205 3.1 55.8 1.0 HE22 A:GLN84 3.3 31.0 1.0 HO2 A:EDO205 3.4 64.9 1.0 O2 A:EDO205 3.6 54.1 1.0 HZ2 A:TRP75 3.8 29.6 1.0 C2 A:EDO205 3.8 46.4 1.0 NE2 A:GLN84 3.8 25.8 1.0 CE2 A:TRP75 4.0 22.4 1.0 CD1 A:TRP75 4.0 23.2 1.0 OE1 A:GLN84 4.0 29.3 1.0 HD1 A:TRP75 4.1 27.9 1.0 H21 A:EDO205 4.1 55.8 1.0 CD A:GLN84 4.2 28.6 1.0 CZ2 A:TRP75 4.2 24.6 1.0 HE21 A:GLN84 4.3 31.0 1.0 HZ3 A:TRP81 4.4 41.3 0.4 CZ3 A:TRP81 4.8 34.4 0.4

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