Chlorine in PDB 5ku9: Crystal Structure of MCL1 with Compound 1

All present enzymatic activity of Crystal Structure of MCL1 with Compound 1:
3.6.1.11;

The structure of Crystal Structure of MCL1 with Compound 1, PDB code: 5ku9 was solved by A.D.Ferguson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.39 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.381, 60.647, 69.087, 90.00, 121.15, 90.00
R / Rfree (%)	18.7 / 24.1

The structure of Crystal Structure of MCL1 with Compound 1 also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Chlorine atom in the Crystal Structure of MCL1 with Compound 1 (pdb code 5ku9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of MCL1 with Compound 1, PDB code: 5ku9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of MCL1 with Compound 1


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 MCL1 with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:57.4 occ:1.00 CL A:6XJ402 0.0 57.4 1.0 C9 A:6XJ402 1.7 46.6 1.0 C10 A:6XJ402 2.7 40.9 1.0 C8 A:6XJ402 2.7 42.2 1.0 CL1 A:6XJ402 3.1 40.6 1.0 CD2 A:PHE270 3.5 36.4 1.0 CA A:MET250 3.7 37.1 1.0 CE A:MET231 3.9 45.0 1.0 CG1 A:VAL249 4.0 42.9 1.0 C7 A:6XJ402 4.0 38.0 1.0 C5 A:6XJ402 4.0 36.4 1.0 CE2 A:PHE270 4.0 41.5 1.0 N A:MET250 4.1 37.9 1.0 CG A:MET250 4.1 44.5 1.0 CG A:PHE270 4.2 33.3 1.0 CD1 A:LEU267 4.3 28.4 1.0 O A:VAL249 4.3 41.5 1.0 C A:VAL249 4.4 42.5 1.0 CB A:MET250 4.4 39.6 1.0 C6 A:6XJ402 4.5 34.1 1.0 CB A:PHE270 4.5 30.0 1.0 O A:MET250 4.6 36.7 1.0 C A:MET250 4.6 38.9 1.0 SD A:MET231 4.7 48.1 1.0 CZ A:PHE270 5.0 40.6 1.0 CB A:VAL253 5.0 35.3 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of MCL1 with Compound 1


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 MCL1 with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:40.6 occ:1.00 CL1 A:6XJ402 0.0 40.6 1.0 C8 A:6XJ402 1.7 42.2 1.0 C9 A:6XJ402 2.7 46.6 1.0 C7 A:6XJ402 2.7 38.0 1.0 CL A:6XJ402 3.1 57.4 1.0 CB A:PHE270 3.5 30.0 1.0 O A:THR266 3.6 23.9 1.0 CG2 A:THR266 3.8 24.3 1.0 CA A:LEU267 3.8 23.7 1.0 C A:THR266 3.9 25.3 1.0 N A:LEU267 4.0 23.6 1.0 C10 A:6XJ402 4.0 40.9 1.0 C6 A:6XJ402 4.0 34.1 1.0 CG A:PHE270 4.1 33.3 1.0 CG2 A:VAL253 4.2 35.0 1.0 CE1 A:PHE228 4.3 32.6 1.0 CD2 A:PHE270 4.5 36.4 1.0 CB A:VAL253 4.5 35.3 1.0 C5 A:6XJ402 4.5 36.4 1.0 C15 A:6XJ402 4.6 38.4 1.0 CB A:THR266 4.7 24.7 1.0 CB A:LEU267 4.8 23.8 1.0 O A:LEU267 4.8 29.0 1.0 C A:LEU267 4.8 28.5 1.0 CA A:PHE270 4.9 28.1 1.0 CD1 A:LEU267 4.9 28.4 1.0 CZ A:PHE228 4.9 29.3 1.0 CA A:THR266 4.9 24.2 1.0 CD1 A:PHE270 4.9 38.3 1.0 SD A:MET231 5.0 48.1 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of MCL1 with Compound 1


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 MCL1 with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:61.5 occ:1.00 CL B:6XJ401 0.0 61.5 1.0 C9 B:6XJ401 1.7 52.4 1.0 C10 B:6XJ401 2.7 48.7 1.0 C8 B:6XJ401 2.7 47.7 1.0 CL1 B:6XJ401 3.2 50.3 1.0 CD2 B:PHE270 3.5 52.3 1.0 CE2 B:PHE270 3.7 56.2 1.0 CG B:MET250 3.9 59.1 1.0 CA B:MET250 3.9 50.4 1.0 C5 B:6XJ401 4.0 47.8 1.0 C7 B:6XJ401 4.0 46.1 1.0 CD1 B:LEU267 4.0 49.7 1.0 SD B:MET231 4.2 72.7 1.0 CG B:PHE270 4.3 52.3 1.0 N B:MET250 4.3 48.9 1.0 CG1 B:VAL249 4.3 53.6 1.0 CB B:MET250 4.4 53.9 1.0 C6 B:6XJ401 4.5 45.9 1.0 O B:VAL249 4.6 53.1 1.0 C B:VAL249 4.6 52.2 1.0 CZ B:PHE270 4.6 55.6 1.0 CE B:MET231 4.7 68.7 1.0 CB B:PHE270 4.8 51.5 1.0 C B:MET250 5.0 53.0 1.0 CB B:VAL249 5.0 54.9 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of MCL1 with Compound 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of MCL1 with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:50.3 occ:1.00 CL1 B:6XJ401 0.0 50.3 1.0 C8 B:6XJ401 1.7 47.7 1.0 C7 B:6XJ401 2.7 46.1 1.0 C9 B:6XJ401 2.7 52.4 1.0 CL B:6XJ401 3.2 61.5 1.0 O B:THR266 3.8 49.8 1.0 CB B:PHE270 3.8 51.5 1.0 CA B:LEU267 3.9 45.8 1.0 C6 B:6XJ401 4.0 45.9 1.0 CG2 B:THR266 4.0 55.4 1.0 C10 B:6XJ401 4.0 48.7 1.0 C B:THR266 4.0 51.0 1.0 N B:LEU267 4.1 46.3 1.0 CG B:PHE270 4.1 52.3 1.0 CE B:MET231 4.2 68.7 1.0 CD2 B:PHE270 4.3 52.3 1.0 C15 B:6XJ401 4.4 51.6 1.0 CD1 B:LEU267 4.4 49.7 1.0 CE1 B:PHE228 4.4 53.0 1.0 CG2 B:VAL253 4.4 56.9 1.0 C5 B:6XJ401 4.5 47.8 1.0 CB B:LEU267 4.6 45.9 1.0 CB B:THR266 4.7 58.5 1.0 SD B:MET231 4.7 72.7 1.0 CB B:VAL253 4.8 56.2 1.0 C14 B:6XJ401 4.9 52.8 1.0 CD1 B:PHE270 4.9 57.4 1.0 C B:LEU267 5.0 51.7 1.0 O B:LEU267 5.0 52.9 1.0 CA B:THR266 5.0 49.4 1.0

J.W.Johannes, S.Bates, C.Beigie, M.A.Belmonte, J.Breen, S.Cao, P.A.Centrella, M.A.Clark, J.W.Cuozzo, C.E.Dumelin, A.D.Ferguson, S.Habeshian, D.Hargreaves, C.Joubran, S.Kazmirski, A.D.Keefe, M.L.Lamb, H.Lan, Y.Li, H.Ma, S.Mlynarski, M.J.Packer, P.B.Rawlins, D.W.Robbins, H.Shen, E.A.Sigel, H.H.Soutter, N.Su, D.M.Troast, H.Wang, K.F.Wickson, C.Wu, Y.Zhang, Q.Zhao, X.Zheng, A.W.Hird. Structure Based Design of Non-Natural Peptidic Macrocyclic Mcl-1 Inhibitors. Acs Med Chem Lett V. 8 239 2017.
ISSN: ISSN 1948-5875
PubMed: 28197319
DOI: 10.1021/ACSMEDCHEMLETT.6B00464