Fluorine in PDB 7wn5: Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor Y13142

The structure of Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor Y13142, PDB code: 7wn5 was solved by J.Li, C.Zhang, H.Xu, X.Zhuang, X.Wu, Y.Zhang, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.71 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.979, 63.61, 72.14, 90, 90, 90
R / Rfree (%)	23 / 26.9

The structure of Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor Y13142 also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor Y13142 (pdb code 7wn5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor Y13142, PDB code: 7wn5:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor Y13142


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor Y13142 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:39.4 occ:1.00 FBJ A:JGL501 0.0 39.4 1.0 CBE A:JGL501 1.3 32.5 1.0 CBF A:JGL501 2.3 35.9 1.0 CBD A:JGL501 2.4 27.4 1.0 OBC A:JGL501 2.7 22.3 1.0 CAS A:JGL501 3.4 18.0 1.0 CE1 A:HIS433 3.5 28.6 1.0 OAG A:JGL501 3.5 15.3 1.0 CBG A:JGL501 3.5 36.5 1.0 CBI A:JGL501 3.6 29.2 1.0 CAJ A:JGL501 3.7 17.4 1.0 CAR A:JGL501 3.8 17.1 1.0 CAH A:JGL501 3.8 16.3 1.0 NE2 A:HIS433 4.0 30.1 1.0 CBH A:JGL501 4.1 34.0 1.0 NAT A:JGL501 4.1 18.7 1.0 CAQ A:JGL501 4.3 16.0 1.0 CAA A:JGL501 4.4 14.8 1.0 NAV A:JGL501 4.4 18.9 1.0 FBK A:JGL501 4.6 49.3 1.0 ND1 A:HIS433 4.6 23.5 1.0 CAU A:JGL501 4.7 18.8 1.0 CAK A:JGL501 4.8 14.8 1.0 CAI A:JGL501 4.9 15.1 1.0 CAF A:JGL501 4.9 14.5 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor Y13142


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor Y13142 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:49.3 occ:1.00 FBK A:JGL501 0.0 49.3 1.0 CBG A:JGL501 1.4 36.5 1.0 CBF A:JGL501 2.3 35.9 1.0 CBH A:JGL501 2.4 34.0 1.0 CB A:ASP434 3.4 23.7 1.0 CBE A:JGL501 3.6 32.5 1.0 CBI A:JGL501 3.7 29.2 1.0 OD2 A:ASP434 4.0 34.5 1.0 CG A:ASP434 4.1 27.0 1.0 CBD A:JGL501 4.1 27.4 1.0 SD A:MET438 4.6 22.0 1.0 FBJ A:JGL501 4.6 39.4 1.0 CA A:ASP434 4.7 19.5 1.0 C A:ASP434 4.9 16.9 1.0 N A:VAL435 4.9 15.2 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor Y13142


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor Y13142 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:37.4 occ:1.00 FBJ B:JGL501 0.0 37.4 1.0 CBE B:JGL501 1.3 31.6 1.0 CBF B:JGL501 2.3 36.0 1.0 CBD B:JGL501 2.4 27.0 1.0 OBC B:JGL501 2.7 22.5 1.0 CE1 B:HIS433 3.4 27.1 1.0 CAS B:JGL501 3.4 18.1 1.0 CBG B:JGL501 3.5 36.7 1.0 OAG B:JGL501 3.5 16.0 1.0 CBI B:JGL501 3.6 29.1 1.0 CAJ B:JGL501 3.7 17.5 1.0 CAR B:JGL501 3.8 17.0 1.0 CAH B:JGL501 3.9 16.7 1.0 NE2 B:HIS433 4.0 28.7 1.0 CBH B:JGL501 4.0 33.9 1.0 NAT B:JGL501 4.2 18.6 1.0 CAQ B:JGL501 4.3 15.5 1.0 CAA B:JGL501 4.4 14.7 1.0 NAV B:JGL501 4.5 19.2 1.0 ND1 B:HIS433 4.6 22.4 1.0 FBK B:JGL501 4.6 51.1 1.0 CAU B:JGL501 4.7 18.6 1.0 CAK B:JGL501 4.8 14.7 1.0 CAI B:JGL501 4.9 15.2 1.0 CAF B:JGL501 5.0 14.2 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor Y13142


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor Y13142 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:51.1 occ:1.00 FBK B:JGL501 0.0 51.1 1.0 CBG B:JGL501 1.4 36.7 1.0 CBF B:JGL501 2.3 36.0 1.0 CBH B:JGL501 2.4 33.9 1.0 CB B:ASP434 3.4 23.8 1.0 CBE B:JGL501 3.6 31.6 1.0 CBI B:JGL501 3.7 29.1 1.0 OD2 B:ASP434 4.0 34.4 1.0 CG B:ASP434 4.1 27.3 1.0 CBD B:JGL501 4.1 27.0 1.0 SD B:MET438 4.5 22.1 1.0 FBJ B:JGL501 4.6 37.4 1.0 CA B:ASP434 4.7 20.2 1.0 C B:ASP434 4.8 17.0 1.0 N B:VAL435 4.9 15.6 1.0

J.Li, C.Zhang, H.Xu, C.Wang, R.Dong, H.Shen, X.Zhuang, X.Chen, Q.Li, J.Lu, M.Zhang, X.Wu, K.M.Loomes, Y.Zhou, Y.Zhang, J.Liu, Y.Xu. Structure-Based Discovery and Optimization of Furo[3,2- C ]Pyridin-4(5 H )-One Derivatives As Potent and Second Bromodomain (BD2)-Selective Bromo and Extra Terminal Domain (Bet) Inhibitors. J.Med.Chem. V. 65 5760 2022.
ISSN: ISSN 0022-2623
PubMed: 35333526
DOI: 10.1021/ACS.JMEDCHEM.2C00100