Iodine in PDB 5s9r: Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Bms-986158, 2-{3-(1,4-Dimethyl-1H-1,2,3-Triazol-5-Yl)-5-[(S)- (Oxan-4-Yl)(Phenyl)Methyl]-5H-Pyrido[3,2-B]Indol-7-Yl}Propan-2-Ol

The structure of Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Bms-986158, 2-{3-(1,4-Dimethyl-1H-1,2,3-Triazol-5-Yl)-5-[(S)- (Oxan-4-Yl)(Phenyl)Methyl]-5H-Pyrido[3,2-B]Indol-7-Yl}Propan-2-Ol, PDB code: 5s9r was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.54 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.6, 48.5, 58.1, 90, 90, 90
R / Rfree (%)	20.8 / 23.1

The binding sites of Iodine atom in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Bms-986158, 2-{3-(1,4-Dimethyl-1H-1,2,3-Triazol-5-Yl)-5-[(S)- (Oxan-4-Yl)(Phenyl)Methyl]-5H-Pyrido[3,2-B]Indol-7-Yl}Propan-2-Ol (pdb code 5s9r). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Bms-986158, 2-{3-(1,4-Dimethyl-1H-1,2,3-Triazol-5-Yl)-5-[(S)- (Oxan-4-Yl)(Phenyl)Methyl]-5H-Pyrido[3,2-B]Indol-7-Yl}Propan-2-Ol, PDB code: 5s9r:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Bms-986158, 2-{3-(1,4-Dimethyl-1H-1,2,3-Triazol-5-Yl)-5-[(S)- (Oxan-4-Yl)(Phenyl)Methyl]-5H-Pyrido[3,2-B]Indol-7-Yl}Propan-2-Ol


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Bms-986158, 2-{3-(1,4-Dimethyl-1H-1,2,3-Triazol-5-Yl)-5-[(S)- (Oxan-4-Yl)(Phenyl)Methyl]-5H-Pyrido[3,2-B]Indol-7-Yl}Propan-2-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:42.8 occ:0.50 H68 A:YWA301 3.2 22.3 0.0 H70 A:YWA301 3.2 22.0 0.0 H53 A:YWA301 3.2 26.0 0.0 N A:ILE146 3.5 17.9 1.0 H52 A:YWA301 3.7 28.2 0.0 CG2 A:ILE146 3.8 20.7 1.0 C36 A:YWA301 3.8 22.3 1.0 N A:ASP145 3.8 20.2 1.0 H67 A:YWA301 3.9 22.3 0.0 C25 A:YWA301 3.9 26.0 1.0 C37 A:YWA301 4.0 22.0 1.0 CB A:ILE146 4.0 18.5 1.0 C24 A:YWA301 4.1 28.2 1.0 CB A:ASP144 4.1 22.4 1.0 CB A:ASP145 4.1 21.3 1.0 H48 A:YWA301 4.3 18.7 0.0 CA A:ASP145 4.3 19.5 1.0 CA A:ILE146 4.4 16.9 1.0 C A:ASP145 4.4 21.7 1.0 C A:ASP144 4.5 22.7 1.0 CG A:ASP144 4.6 31.6 1.0 CA A:ASP144 4.7 20.8 1.0 C19 A:YWA301 4.7 18.7 1.0 H69 A:YWA301 4.8 22.0 0.0 OD2 A:ASP145 4.8 33.5 1.0 CG A:ASP145 4.9 27.9 1.0 OD2 A:ASP144 4.9 27.3 1.0 C20 A:YWA301 5.0 22.2 1.0

Iodine binding site 2 out of 3 in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Bms-986158, 2-{3-(1,4-Dimethyl-1H-1,2,3-Triazol-5-Yl)-5-[(S)- (Oxan-4-Yl)(Phenyl)Methyl]-5H-Pyrido[3,2-B]Indol-7-Yl}Propan-2-Ol


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Bms-986158, 2-{3-(1,4-Dimethyl-1H-1,2,3-Triazol-5-Yl)-5-[(S)- (Oxan-4-Yl)(Phenyl)Methyl]-5H-Pyrido[3,2-B]Indol-7-Yl}Propan-2-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:38.1 occ:0.50 N A:GLN59 3.4 25.3 1.0 CA A:ARG58 3.9 18.2 1.0 O A:GLN59 4.0 33.1 1.0 C A:ARG58 4.1 24.4 1.0 CB A:ARG58 4.2 17.1 1.0 CA A:GLN59 4.4 27.5 1.0 CB A:GLN59 4.5 30.0 1.0 C A:GLN59 4.6 31.3 1.0 O A:LYS57 4.7 18.9 1.0

Iodine binding site 3 out of 3 in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Bms-986158, 2-{3-(1,4-Dimethyl-1H-1,2,3-Triazol-5-Yl)-5-[(S)- (Oxan-4-Yl)(Phenyl)Methyl]-5H-Pyrido[3,2-B]Indol-7-Yl}Propan-2-Ol


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Bms-986158, 2-{3-(1,4-Dimethyl-1H-1,2,3-Triazol-5-Yl)-5-[(S)- (Oxan-4-Yl)(Phenyl)Methyl]-5H-Pyrido[3,2-B]Indol-7-Yl}Propan-2-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:41.5 occ:0.50 CB A:ASN54 3.4 28.9 1.0 N A:ASN54 3.5 24.0 1.0 CA A:ASN52 3.7 20.1 1.0 C A:ASN52 3.7 23.6 1.0 CB A:ASN52 3.8 19.9 1.0 CA A:ASN54 3.9 23.7 1.0 N A:PRO53 4.1 22.3 1.0 O A:ASN52 4.1 21.3 1.0 C A:ASN54 4.3 27.6 1.0 N A:LYS55 4.3 23.9 1.0 CD A:PRO53 4.4 25.4 1.0 C A:PRO53 4.6 28.0 1.0 CG A:LYS55 4.6 33.2 1.0 CA A:PRO53 4.9 23.5 1.0 CG A:PRO53 5.0 29.4 1.0

A.V.Gavai, D.Norris, G.Delucca, D.Tortolani, J.S.Tokarski, D.Dodd, D.O'malley, Y.Zhao, C.Quesnelle, P.Gill, W.Vaccaro, T.Huynh, V.Ahuja, W.-C.Han, C.Mussari, L.Harikrishnan, M.Kamau, M.Poss, S.Sheriff, C.Yan, F.Marsilio, K.Menard, M.-L.Wen, R.Rampulla, D.-R.Wu, J.Li, H.Zhang, P.Li, D.Sun, H.Yip, Y.Zhang, A.Mathur, H.Zhang, C.Huang, Z., Yang, A.Ranasinghe, G.Everlof, N.Raghavan, C.K.Tye, S.Wee, J.T.Hunt, G.D.Vite, R.Westhouse, F.Y.Lee. Discovery and Preclinical Pharmacology of An Oral Bromodomain and Extra-Terminal (Bet) Inhibitor Using Scaffold-Hopping and Structure-Guided Drug Design J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACS.JMEDCHEM.1C00625