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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
TitleCrystal structure of Bcl-2 in complex with the novel orally active inhibitor S55746
ComponentsApoptosis 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
KeywordsAPOPTOSIS / APOPTOSIS-INHIBITOR COMPLEX / BCL-2 / BH3-mimetics
Function / homology
Function and homology information


channel inhibitor activity / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / melanin metabolic process ...channel inhibitor activity / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / melanin metabolic process / myeloid cell apoptotic process / cochlear nucleus development / osteoblast proliferation / mesenchymal cell development / retinal cell programmed cell death / positive regulation of neuron maturation / negative regulation of osteoblast proliferation / gland morphogenesis / renal system process / regulation of cell-matrix adhesion / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / negative regulation of calcium ion transport into cytosol / stem cell development / lymphoid progenitor cell differentiation / T cell apoptotic process / melanocyte differentiation / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / B cell apoptotic process / regulation of nitrogen utilization / negative regulation of T cell apoptotic process / glomerulus development / positive regulation of multicellular organism growth / metanephros development / Regulation of MITF-M-dependent genes involved in apoptosis / neuron maturation / focal adhesion assembly / negative regulation of motor neuron apoptotic process / regulation of viral genome replication / oocyte development / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-B / response to iron ion / negative regulation of ossification / motor neuron apoptotic process / negative regulation of mitochondrial depolarization / axon regeneration / epithelial cell apoptotic process / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / organ growth / negative regulation of B cell apoptotic process / hair follicle morphogenesis / branching involved in ureteric bud morphogenesis / digestive tract morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / B cell lineage commitment / positive regulation of smooth muscle cell migration / negative regulation of G1/S transition of mitotic cell cycle / pore complex / negative regulation of intrinsic apoptotic signaling pathway / T cell homeostasis / BH3 domain binding / B cell homeostasis / humoral immune response / B cell proliferation / negative regulation of apoptotic signaling pathway / negative regulation of anoikis / regulation of calcium ion transport / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Activation of BAD and translocation to mitochondria / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hematopoietic stem cell differentiation / behavioral fear response / response to glucocorticoid / cellular response to glucose starvation / ovarian follicle development / skeletal muscle fiber development / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / homeostasis of number of cells within a tissue / positive regulation of B cell proliferation / response to cytokine / negative regulation of autophagy / regulation of transmembrane transporter activity / reactive oxygen species metabolic process / axonogenesis / ossification / release of cytochrome c from mitochondria / negative regulation of cell migration / regulation of mitochondrial membrane potential
Similarity search - Function
Apoptosis regulator, Bcl-2 / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...Apoptosis regulator, Bcl-2 / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Chem-F3Q / Apoptosis regulator Bcl-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCasara, 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.
CitationJournal: Oncotarget / Year: 2018
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
DepositionMay 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9472
Polymers20,2371
Non-polymers7111
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.090, 46.900, 85.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 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 / Bcl2-L-1 / Apoptosis regulator Bcl-X


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.) Homo sapiens (human) / Gene: BCL2, BCL2L1, BCL2L, BCLX / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P10415
#2: Chemical ChemComp-F3Q / ~{N}-(4-hydroxyphenyl)-3-[6-[[(3~{S})-3-(morpholin-4-ylmethyl)-3,4-dihydro-1~{H}-isoquinolin-2-yl]carbonyl]-1,3-benzodioxol-5-yl]-~{N}-phenyl-5,6,7,8-tetrahydroindolizine-1-carboxamide


Mass: 710.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H42N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.76 Å3/Da / Density % sol: 29.7 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 0.1 M sodium acetate buffer pH 5.25, 20% Jeffamine600, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimless0.5.17data scaling
MOLREP11.5.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W3L

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
RfactorNum. reflection% reflectionSelection details
Rfree0.19439 1447 5.1 %RANDOM
Rwork0.17818 ---
obs0.17904 26743 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å2-0 Å20 Å2
2---0.62 Å20 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1188 0 53 151 1392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0141306
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171083
X-RAY DIFFRACTIONr_angle_refined_deg1.821.7141775
X-RAY DIFFRACTIONr_angle_other_deg1.1391.6612479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.365148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.06720.46586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3515203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2621514
X-RAY DIFFRACTIONr_chiral_restr0.090.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021507
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.292.093582
X-RAY DIFFRACTIONr_mcbond_other2.2522.085581
X-RAY DIFFRACTIONr_mcangle_it3.2843.118726
X-RAY DIFFRACTIONr_mcangle_other3.2973.122727
X-RAY DIFFRACTIONr_scbond_it3.542.498724
X-RAY DIFFRACTIONr_scbond_other3.5382.497725
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3163.5951044
X-RAY DIFFRACTIONr_long_range_B_refined8.33643.8366794
X-RAY DIFFRACTIONr_long_range_B_other8.33443.4466649
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.475 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.266 211 -
Rwork0.256 3844 -
obs--99.8 %

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