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- PDB-6gl8: Crystal structure of Bcl-2 in complex with the novel orally activ... -
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Basic information
Entry | Database: PDB / ID: 6gl8 | ||||||
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Title | Crystal structure of Bcl-2 in complex with the novel orally active inhibitor S55746 | ||||||
![]() | Apoptosis regulator Bcl-2,Apoptosis regulator Bcl-2,Apoptosis regulator Bcl-2,Bcl-2-like protein 1,Apoptosis regulator Bcl-2,Apoptosis regulator Bcl-2,Apoptosis regulator Bcl-2 | ||||||
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Function / homology | ![]() negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation ...negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation / myeloid cell apoptotic process / osteoblast proliferation / cochlear nucleus development / mesenchymal cell development / retinal cell programmed cell death / positive regulation of neuron maturation / negative regulation of osteoblast proliferation / gland morphogenesis / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Casara, P. / Davidson, J. / Claperon, A. / Le Toumelin-Braizat, G. / Vogler, M. / Bruno, A. / Chanrion, M. / Lysiak-Auvity, G. / Le Diguarher, T. / Starck, J.B. ...Casara, P. / Davidson, J. / Claperon, A. / Le Toumelin-Braizat, G. / Vogler, M. / Bruno, A. / Chanrion, M. / Lysiak-Auvity, G. / Le Diguarher, T. / Starck, J.B. / Chen, I. / Whitehead, N. / Graham, C. / Matassova, N. / Dokurno, P. / Pedder, C. / Wang, Y. / Qiu, S. / Girard, A.M. / Schneider, E. / Grave, F. / Studeny, A. / Guasconi, G. / Rocchetti, F. / Maiga, S. / Henlin, J.M. / Colland, F. / Kraus-Berthier, L. / Le Gouill, S. / Dyer, M.J.S. / Hubbard, R. / Wood, M. / Amiot, M. / Cohen, G.M. / Hickman, J.A. / Morris, E. / Murray, J. / Geneste, O. | ||||||
![]() | ![]() Title: S55746 is a novel orally active BCL-2 selective and potent inhibitor that impairs hematological tumor growth. Authors: Casara, P. / Davidson, J. / Claperon, A. / Le Toumelin-Braizat, G. / Vogler, M. / Bruno, A. / Chanrion, M. / Lysiak-Auvity, G. / Le Diguarher, T. / Starck, J.B. / Chen, I. / Whitehead, N. / ...Authors: Casara, P. / Davidson, J. / Claperon, A. / Le Toumelin-Braizat, G. / Vogler, M. / Bruno, A. / Chanrion, M. / Lysiak-Auvity, G. / Le Diguarher, T. / Starck, J.B. / Chen, I. / Whitehead, N. / Graham, C. / Matassova, N. / Dokurno, P. / Pedder, C. / Wang, Y. / Qiu, S. / Girard, A.M. / Schneider, E. / Grave, F. / Studeny, A. / Guasconi, G. / Rocchetti, F. / Maiga, S. / Henlin, J.M. / Colland, F. / Kraus-Berthier, L. / Le Gouill, S. / Dyer, M.J.S. / Hubbard, R. / Wood, M. / Amiot, M. / Cohen, G.M. / Hickman, J.A. / Morris, E. / Murray, J. / Geneste, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 51.5 KB | Display | ![]() |
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PDB format | ![]() | 34.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2w3lS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20236.555 Da / Num. of mol.: 1 Mutation: L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, ...Mutation: L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-F3Q / ~{ |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.76 Å3/Da / Density % sol: 29.7 % |
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Crystal grow![]() | Temperature: 284 K / Method: vapor diffusion, hanging drop / pH: 5.25 Details: 0.1 M sodium acetate buffer pH 5.25, 20% Jeffamine600, 10% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.39→42.5 Å / Num. obs: 28969 / % possible obs: 98.9 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.019 / Rrim(I) all: 0.039 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.39→1.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1967 / CC1/2: 0.877 / Rpim(I) all: 0.31 / Rrim(I) all: 0.63 / % possible all: 91.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2W3L Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.12 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.064 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.1 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→20 Å
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Refine LS restraints |
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