Chlorine in PDB 6bw8: Mcl-1 Complexed with Small Molecules

Protein crystallography data

The structure of Mcl-1 Complexed with Small Molecules, PDB code: 6bw8 was solved by B.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.178, 135.397, 95.750, 90.00, 90.12, 90.00
R / Rfree (%) 23.5 / 25.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Mcl-1 Complexed with Small Molecules (pdb code 6bw8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Mcl-1 Complexed with Small Molecules, PDB code: 6bw8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6bw8

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Chlorine binding site 1 out of 8 in the Mcl-1 Complexed with Small Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Mcl-1 Complexed with Small Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl400

b:43.3
occ:1.00
CL04 A:ECM400 0.0 43.3 1.0
C03 A:ECM400 1.8 40.6 1.0
C05 A:ECM400 2.7 40.9 1.0
C02 A:ECM400 2.8 40.2 1.0
C06 A:ECM400 3.0 41.5 1.0
C01 A:ECM400 3.1 40.6 1.0
CE A:MET250 3.9 39.5 1.0
C07 A:ECM400 4.0 40.8 1.0
C50 A:ECM400 4.0 40.3 1.0
CE2 A:PHE270 4.2 42.6 1.0
CB A:LEU246 4.3 47.9 1.0
CD2 A:PHE270 4.3 42.1 1.0
CD1 A:LEU246 4.4 48.0 1.0
CD1 A:LEU290 4.4 43.5 1.0
CG2 A:VAL274 4.5 41.7 1.0
C08 A:ECM400 4.6 40.5 1.0
CB A:MET250 4.6 43.6 1.0
CD1 A:LEU235 4.6 49.8 1.0
O A:LEU246 4.7 47.4 1.0
CG A:LEU246 4.8 48.3 1.0
CD2 A:LEU246 4.8 48.5 1.0
CG A:MET250 4.8 42.3 1.0

Chlorine binding site 2 out of 8 in 6bw8

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Chlorine binding site 2 out of 8 in the Mcl-1 Complexed with Small Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Mcl-1 Complexed with Small Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl400

b:43.1
occ:1.00
CL40 A:ECM400 0.0 43.1 1.0
C39 A:ECM400 1.7 42.5 1.0
C41 A:ECM400 2.7 45.4 1.0
C38 A:ECM400 2.7 43.9 1.0
C42 A:ECM400 3.1 47.2 1.0
O A:ALA227 3.3 45.5 1.0
CD1 A:PHE228 3.3 44.5 1.0
CB A:MET231 3.5 49.9 1.0
C A:ALA227 3.6 45.2 1.0
C48 A:ECM400 3.6 47.5 1.0
CA A:PHE228 3.8 45.4 1.0
N A:PHE228 3.8 45.5 1.0
CE1 A:PHE228 3.8 44.1 1.0
C43 A:ECM400 3.9 46.9 1.0
C49 A:ECM400 3.9 48.0 1.0
CG A:MET231 4.0 48.5 1.0
C37 A:ECM400 4.0 43.5 1.0
C35 A:ECM400 4.0 44.0 1.0
CB A:ALA227 4.1 45.0 1.0
SD A:MET231 4.4 47.5 1.0
CG A:PHE228 4.4 44.5 1.0
CE1 A:PHE270 4.4 42.6 1.0
CA A:ALA227 4.4 45.4 1.0
N47 A:ECM400 4.5 48.6 1.0
C44 A:ECM400 4.5 46.7 1.0
C36 A:ECM400 4.5 41.5 1.0
N45 A:ECM400 4.6 48.6 1.0
CB A:PHE228 4.7 45.0 1.0
CZ A:PHE270 4.7 42.9 1.0
CD1 A:PHE270 4.8 42.1 1.0
C A:PHE228 4.8 45.9 1.0
CA A:MET231 4.8 51.6 1.0
O A:PHE228 4.9 46.1 1.0

Chlorine binding site 3 out of 8 in 6bw8

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Chlorine binding site 3 out of 8 in the Mcl-1 Complexed with Small Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Mcl-1 Complexed with Small Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl400

b:45.2
occ:1.00
CL04 B:ECM400 0.0 45.2 1.0
C03 B:ECM400 1.8 44.6 1.0
C05 B:ECM400 2.7 44.2 1.0
C02 B:ECM400 2.7 44.2 1.0
C06 B:ECM400 3.0 44.7 1.0
C01 B:ECM400 3.1 44.9 1.0
CE B:MET250 3.7 46.2 1.0
CD2 B:LEU246 3.9 48.0 1.0
CD1 B:LEU246 4.0 47.8 1.0
CD1 B:LEU235 4.0 47.7 1.0
C07 B:ECM400 4.0 43.4 1.0
C50 B:ECM400 4.0 43.4 1.0
CB B:LEU246 4.0 48.0 1.0
CB B:MET250 4.2 45.7 1.0
CG B:LEU246 4.2 48.3 1.0
CE2 B:PHE270 4.3 45.2 1.0
CD2 B:PHE270 4.4 44.6 1.0
CG B:MET250 4.4 45.1 1.0
O B:LEU246 4.5 47.2 1.0
C08 B:ECM400 4.5 43.6 1.0
SD B:MET250 4.8 45.4 1.0
CA B:MET250 4.8 45.5 1.0
CG2 B:VAL274 4.9 44.9 1.0

Chlorine binding site 4 out of 8 in 6bw8

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Chlorine binding site 4 out of 8 in the Mcl-1 Complexed with Small Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Mcl-1 Complexed with Small Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl400

b:42.5
occ:1.00
CL40 B:ECM400 0.0 42.5 1.0
C39 B:ECM400 1.7 42.0 1.0
C38 B:ECM400 2.7 42.0 1.0
C41 B:ECM400 2.7 42.9 1.0
C42 B:ECM400 3.0 42.6 1.0
O B:ALA227 3.1 46.3 1.0
CB B:MET231 3.3 48.5 1.0
SD B:MET231 3.4 48.5 1.0
C B:ALA227 3.5 45.9 1.0
C48 B:ECM400 3.6 45.1 1.0
CD1 B:PHE228 3.7 58.2 1.0
N B:PHE228 3.8 42.4 1.0
CA B:PHE228 3.9 42.8 1.0
C43 B:ECM400 3.9 43.9 1.0
C49 B:ECM400 3.9 45.2 1.0
CG B:MET231 3.9 48.5 1.0
C37 B:ECM400 4.0 42.0 1.0
CB B:ALA227 4.0 45.6 1.0
C35 B:ECM400 4.0 42.7 1.0
CE B:MET231 4.1 49.2 1.0
CE1 B:PHE228 4.2 56.8 1.0
CA B:ALA227 4.3 46.1 1.0
N47 B:ECM400 4.4 44.0 1.0
C36 B:ECM400 4.5 42.7 1.0
C44 B:ECM400 4.5 42.5 1.0
CA B:MET231 4.6 49.5 1.0
N45 B:ECM400 4.6 43.1 1.0
N B:MET231 4.6 48.8 1.0
CG B:PHE228 4.7 41.8 1.0
C B:PHE228 4.8 43.5 1.0
O B:PHE228 4.9 44.0 1.0
CB B:PHE228 4.9 42.4 1.0
CE1 B:PHE270 4.9 44.6 1.0

Chlorine binding site 5 out of 8 in 6bw8

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Chlorine binding site 5 out of 8 in the Mcl-1 Complexed with Small Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Mcl-1 Complexed with Small Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl400

b:47.1
occ:1.00
CL04 C:ECM400 0.0 47.1 1.0
C03 C:ECM400 1.8 47.3 1.0
C05 C:ECM400 2.7 47.5 1.0
C02 C:ECM400 2.8 48.8 1.0
C06 C:ECM400 3.0 46.4 1.0
C01 C:ECM400 3.1 49.7 1.0
CD1 C:LEU246 3.9 54.2 1.0
CB C:LEU246 3.9 54.8 1.0
C07 C:ECM400 4.0 48.6 1.0
C50 C:ECM400 4.0 49.6 1.0
CE2 C:PHE270 4.1 46.7 1.0
CD2 C:PHE270 4.2 47.4 1.0
CE C:MET250 4.3 48.3 1.0
CG C:LEU246 4.3 54.4 1.0
CD2 C:LEU246 4.4 54.7 1.0
CG2 C:VAL274 4.5 48.4 1.0
C08 C:ECM400 4.6 49.3 1.0
CD1 C:LEU235 4.6 48.6 1.0
O C:LEU246 4.6 55.5 1.0
CB C:MET250 4.8 49.6 1.0
CD1 C:LEU290 4.9 51.5 1.0

Chlorine binding site 6 out of 8 in 6bw8

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Chlorine binding site 6 out of 8 in the Mcl-1 Complexed with Small Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Mcl-1 Complexed with Small Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl400

b:46.8
occ:1.00
CL40 C:ECM400 0.0 46.8 1.0
C39 C:ECM400 1.7 47.5 1.0
C38 C:ECM400 2.7 47.4 1.0
C41 C:ECM400 2.7 47.6 1.0
C42 C:ECM400 3.1 46.3 1.0
O C:ALA227 3.1 48.6 1.0
C C:ALA227 3.4 49.6 1.0
CD1 C:PHE228 3.5 49.6 1.0
CB C:MET231 3.6 46.8 1.0
N C:PHE228 3.7 48.4 1.0
CA C:PHE228 3.7 48.7 1.0
C48 C:ECM400 3.7 45.9 1.0
CE C:MET231 3.7 46.9 1.0
C43 C:ECM400 3.8 46.1 1.0
CB C:ALA227 4.0 52.1 1.0
CE1 C:PHE270 4.0 47.0 1.0
C37 C:ECM400 4.0 47.8 1.0
CE1 C:PHE228 4.0 50.0 1.0
C35 C:ECM400 4.0 48.5 1.0
C49 C:ECM400 4.1 45.4 1.0
CG C:MET231 4.3 46.8 1.0
C44 C:ECM400 4.3 46.7 1.0
CA C:ALA227 4.3 50.8 1.0
CD1 C:PHE270 4.3 47.7 1.0
CZ C:PHE270 4.4 46.5 1.0
CG C:PHE228 4.5 50.1 1.0
N47 C:ECM400 4.5 45.6 1.0
C36 C:ECM400 4.5 48.5 1.0
N45 C:ECM400 4.6 45.9 1.0
C C:PHE228 4.7 48.4 1.0
CB C:PHE228 4.7 49.7 1.0
SD C:MET231 4.7 46.3 1.0
O C:PHE228 4.8 49.2 1.0
CA C:MET231 4.9 46.5 1.0
CG C:PHE270 4.9 47.9 1.0
N C:MET231 5.0 46.6 1.0

Chlorine binding site 7 out of 8 in 6bw8

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Chlorine binding site 7 out of 8 in the Mcl-1 Complexed with Small Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Mcl-1 Complexed with Small Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl400

b:51.7
occ:1.00
CL04 D:ECM400 0.0 51.7 1.0
C03 D:ECM400 1.8 52.4 1.0
C05 D:ECM400 2.7 52.6 1.0
C02 D:ECM400 2.7 52.4 1.0
C06 D:ECM400 3.0 52.5 1.0
C01 D:ECM400 3.1 51.6 1.0
CE2 D:PHE270 4.0 51.8 1.0
C07 D:ECM400 4.0 52.8 1.0
C50 D:ECM400 4.0 52.5 1.0
CD2 D:PHE270 4.0 51.4 1.0
CD1 D:LEU246 4.0 49.9 1.0
CE D:MET250 4.1 48.5 1.0
CD1 D:LEU290 4.2 48.1 1.0
CG2 D:VAL274 4.2 49.9 1.0
C08 D:ECM400 4.5 52.6 1.0
CD2 D:LEU246 4.6 51.4 1.0
CB D:LEU246 4.7 51.1 1.0
CG D:LEU246 4.7 50.5 1.0
CD1 D:LEU235 4.8 52.1 1.0
CG D:MET250 4.9 49.8 1.0

Chlorine binding site 8 out of 8 in 6bw8

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Chlorine binding site 8 out of 8 in the Mcl-1 Complexed with Small Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Mcl-1 Complexed with Small Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl400

b:55.9
occ:1.00
CL40 D:ECM400 0.0 55.9 1.0
C39 D:ECM400 1.7 55.5 1.0
C41 D:ECM400 2.7 56.9 1.0
C38 D:ECM400 2.7 55.6 1.0
O D:ALA227 2.9 58.1 1.0
C42 D:ECM400 3.0 57.2 1.0
C D:ALA227 3.1 57.8 1.0
CB D:ALA227 3.3 58.0 1.0
N D:PHE228 3.6 56.1 1.0
CD1 D:PHE228 3.6 54.2 1.0
C48 D:ECM400 3.7 59.4 1.0
CB D:MET231 3.7 55.2 1.0
C43 D:ECM400 3.7 59.3 1.0
CA D:ALA227 3.8 58.1 1.0
CE D:MET231 3.8 54.5 1.0
CA D:PHE228 3.9 55.1 1.0
C37 D:ECM400 4.0 55.6 1.0
C35 D:ECM400 4.0 56.9 1.0
C49 D:ECM400 4.1 57.6 1.0
CE1 D:PHE228 4.2 53.8 1.0
C44 D:ECM400 4.2 57.9 1.0
N47 D:ECM400 4.5 59.1 1.0
N45 D:ECM400 4.5 59.0 1.0
C36 D:ECM400 4.5 56.2 1.0
CG D:MET231 4.5 54.3 1.0
CG D:PHE228 4.7 53.9 1.0
SD D:MET231 4.8 54.7 1.0
N D:MET231 4.8 56.6 1.0
C D:PHE228 4.8 55.2 1.0
CA D:MET231 4.9 55.8 1.0
CE1 D:PHE270 4.9 52.7 1.0
CB D:PHE228 4.9 54.3 1.0

Reference:

S.Shaw, Z.Bian, B.Zhao, J.C.Tarr, N.Veerasamy, K.O.Jeon, J.Belmar, A.L.Arnold, S.A.Fogarty, E.Perry, J.L.Sensintaffar, D.V.Camper, O.W.Rossanese, T.Lee, E.T.Olejniczak, S.W.Fesik. Optimization of Potent and Selective Tricyclic Indole Diazepinone Myeloid Cell Leukemia-1 Inhibitors Using Structure-Based Design. J. Med. Chem. V. 61 2410 2018.
ISSN: ISSN 1520-4804
PubMed: 29323899
DOI: 10.1021/ACS.JMEDCHEM.7B01155
Page generated: Sat Dec 12 12:47:49 2020

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