Chlorine in PDB 6uve: Crystal Structure of Bcl-Xl Bound to Compound 7: (R)-3-(Benzylthio)-2- (3-(4-Chloro-[1,1':2',1'':3'',1'''-Quaterphenyl]-4'''-Carbonyl)-3-(4- Methylbenzyl)Ureido)Propanoic Acid

The structure of Crystal Structure of Bcl-Xl Bound to Compound 7: (R)-3-(Benzylthio)-2- (3-(4-Chloro-[1,1':2',1'':3'',1'''-Quaterphenyl]-4'''-Carbonyl)-3-(4- Methylbenzyl)Ureido)Propanoic Acid, PDB code: 6uve was solved by M.J.Roy, G.Lessene, P.E.Czabotar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.48 / 2.87
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	148.571, 148.571, 57.448, 90, 90, 90
R / Rfree (%)	21.3 / 25.4

The binding sites of Chlorine atom in the Crystal Structure of Bcl-Xl Bound to Compound 7: (R)-3-(Benzylthio)-2- (3-(4-Chloro-[1,1':2',1'':3'',1'''-Quaterphenyl]-4'''-Carbonyl)-3-(4- Methylbenzyl)Ureido)Propanoic Acid (pdb code 6uve). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Bcl-Xl Bound to Compound 7: (R)-3-(Benzylthio)-2- (3-(4-Chloro-[1,1':2',1'':3'',1'''-Quaterphenyl]-4'''-Carbonyl)-3-(4- Methylbenzyl)Ureido)Propanoic Acid, PDB code: 6uve:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Bcl-Xl Bound to Compound 7: (R)-3-(Benzylthio)-2- (3-(4-Chloro-[1,1':2',1'':3'',1'''-Quaterphenyl]-4'''-Carbonyl)-3-(4- Methylbenzyl)Ureido)Propanoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Bcl-Xl Bound to Compound 7: (R)-3-(Benzylthio)-2- (3-(4-Chloro-[1,1':2',1'':3'',1'''-Quaterphenyl]-4'''-Carbonyl)-3-(4- Methylbenzyl)Ureido)Propanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:89.0 occ:1.00 CL A:QHV301 0.0 89.0 1.0 C36 A:QHV301 1.7 83.6 1.0 C37 A:QHV301 2.7 80.4 1.0 C35 A:QHV301 2.7 81.8 1.0 CA A:PHE146 3.6 48.8 1.0 O A:SER145 3.7 55.1 1.0 N A:PHE146 3.7 49.8 1.0 C A:SER145 3.8 54.6 1.0 CB A:ALA149 3.8 44.7 1.0 C38 A:QHV301 4.0 79.8 1.0 C34 A:QHV301 4.0 81.2 1.0 CB A:PHE146 4.3 49.7 1.0 CB A:ALA104 4.3 95.7 1.0 CB A:SER145 4.4 51.4 1.0 C33 A:QHV301 4.5 79.8 1.0 CE2 A:PHE97 4.6 57.0 1.0 CD1 A:PHE146 4.6 53.7 1.0 C A:PHE146 4.7 56.1 1.0 CA A:SER145 4.7 49.5 1.0 O A:PHE146 4.9 56.8 1.0 O A:ALA142 4.9 58.3 1.0 CG A:PHE146 5.0 50.6 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Bcl-Xl Bound to Compound 7: (R)-3-(Benzylthio)-2- (3-(4-Chloro-[1,1':2',1'':3'',1'''-Quaterphenyl]-4'''-Carbonyl)-3-(4- Methylbenzyl)Ureido)Propanoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Bcl-Xl Bound to Compound 7: (R)-3-(Benzylthio)-2- (3-(4-Chloro-[1,1':2',1'':3'',1'''-Quaterphenyl]-4'''-Carbonyl)-3-(4- Methylbenzyl)Ureido)Propanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:64.6 occ:1.00 CL B:QHV301 0.0 64.6 1.0 C36 B:QHV301 1.7 59.3 1.0 C37 B:QHV301 2.7 57.7 1.0 C35 B:QHV301 2.7 56.6 1.0 O B:SER145 3.6 47.1 1.0 C B:SER145 3.6 46.3 1.0 N B:PHE146 3.7 43.0 1.0 CZ B:PHE105 3.7 99.0 1.0 CA B:PHE146 3.7 41.9 1.0 CE1 B:PHE105 3.9 100.1 1.0 CE2 B:PHE105 3.9 100.9 1.0 O B:HOH408 3.9 63.2 1.0 C38 B:QHV301 4.0 57.5 1.0 C34 B:QHV301 4.0 53.1 1.0 CB B:SER145 4.0 39.5 1.0 CB B:ALA149 4.1 47.4 1.0 CE2 B:PHE97 4.2 45.9 1.0 CD1 B:PHE105 4.3 99.2 1.0 CD2 B:PHE105 4.3 98.3 1.0 CB B:PHE146 4.4 43.0 1.0 CA B:SER145 4.5 38.5 1.0 C33 B:QHV301 4.5 53.6 1.0 CG B:PHE105 4.5 96.4 1.0 O B:ALA142 4.7 46.5 1.0 C B:PHE146 4.9 46.6 1.0 CD2 B:PHE97 4.9 44.1 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Bcl-Xl Bound to Compound 7: (R)-3-(Benzylthio)-2- (3-(4-Chloro-[1,1':2',1'':3'',1'''-Quaterphenyl]-4'''-Carbonyl)-3-(4- Methylbenzyl)Ureido)Propanoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Bcl-Xl Bound to Compound 7: (R)-3-(Benzylthio)-2- (3-(4-Chloro-[1,1':2',1'':3'',1'''-Quaterphenyl]-4'''-Carbonyl)-3-(4- Methylbenzyl)Ureido)Propanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl301 b:75.8 occ:1.00 CL C:QHV301 0.0 75.8 1.0 C36 C:QHV301 1.7 69.3 1.0 C37 C:QHV301 2.7 67.4 1.0 C35 C:QHV301 2.7 66.9 1.0 CE1 C:PHE105 3.4 95.3 1.0 CZ C:PHE105 3.5 94.3 1.0 CA C:PHE146 3.7 49.1 1.0 O C:SER145 3.8 52.0 1.0 N C:PHE146 3.8 48.3 1.0 C C:SER145 3.9 51.2 1.0 CD1 C:PHE105 3.9 95.5 1.0 C38 C:QHV301 4.0 67.4 1.0 C34 C:QHV301 4.0 66.7 1.0 CE2 C:PHE105 4.0 96.5 1.0 CB C:ALA149 4.0 53.7 1.0 CE2 C:PHE97 4.1 55.5 1.0 O C:ALA104 4.2 89.0 1.0 CB C:SER145 4.3 47.5 1.0 CB C:PHE146 4.4 50.9 1.0 CG C:PHE105 4.4 93.4 1.0 CD2 C:PHE105 4.4 94.4 1.0 C33 C:QHV301 4.5 64.3 1.0 C C:ALA104 4.7 88.7 1.0 CA C:SER145 4.7 45.9 1.0 CB C:ALA104 4.8 77.4 1.0 O C:ALA142 4.8 43.3 1.0 CD1 C:PHE146 4.8 55.5 1.0 CD2 C:PHE97 4.9 52.7 1.0 C C:PHE146 4.9 53.6 1.0 CZ C:PHE97 5.0 54.3 1.0

M.J.Roy, A.Vom, T.Okamoto, B.J.Smith, R.W.Birkinshaw, S.Marcuccio, J.B.Baell, H.Yang, H.Abdo, D.C.S.Huang, P.M.Colman, P.E.Czabotar, G.Lessene. Structure-Guided Development of Potent Benzoylurea Inhibitors of Bcl-Xl and Bcl-2 J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACS.JMEDCHEM.0C01771