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- PDB-4c52: Crystal structure of Bcl-xL in complex with benzoylurea compound (39b) -

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Basic information

Entry
Database: PDB / ID: 4c52
TitleCrystal structure of Bcl-xL in complex with benzoylurea compound (39b)
ComponentsBCL-2-LIKE PROTEIN 1
KeywordsAPOPTOSIS
Function / homology
Function and homology information


apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process ...apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / Bcl-2 family protein complex / BH domain binding / NFE2L2 regulating tumorigenic genes / response to cycloheximide / negative regulation of release of cytochrome c from mitochondria / STAT5 activation downstream of FLT3 ITD mutants / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / negative regulation of anoikis / ectopic germ cell programmed cell death / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein localization to plasma membrane / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / ovarian follicle development / release of cytochrome c from mitochondria / negative regulation of autophagy / response to cytokine / epithelial cell proliferation / regulation of cytokinesis / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / endocytosis / RAS processing / male gonad development / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to virus / nuclear membrane / in utero embryonic development / neuron apoptotic process / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Bcl-X / 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-X / 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 / BCL2-like apoptosis inhibitors family profile. / Apoptosis regulator proteins, Bcl-2 family / Bcl-2-like superfamily
Similarity search - Domain/homology
Chem-X0D / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.049 Å
AuthorsRoy, M.J. / Brady, R.M. / Lessene, G. / Colman, P.M. / Czabotar, P.E.
CitationJournal: J.Med.Chem. / Year: 2014
Title: De-Novo Designed Library of Benzoylureas as Inhibitors of Bcl-Xl: Synthesis, Structural and Biochemical Characterization.
Authors: Brady, R.M. / Vom, A. / Roy, M.J. / Toovey, N. / Smith, B.J. / Moss, R.M. / Hazis, E. / Huang, D.C.S. / Parisot, J.P. / Yang, H. / Street, I.P. / Colman, P.M. / Czabotar, P.E. / Baell, J.B. / Lessene, G.
History
DepositionSep 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Apr 29, 2015Group: Data collection
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BCL-2-LIKE PROTEIN 1
B: BCL-2-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,25823
Polymers35,8362
Non-polymers2,42221
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-85.5 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.814, 63.814, 132.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-2002-

HOH

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Components

#1: Protein BCL-2-LIKE PROTEIN 1 / BCL2-L-1 / APOPTOSIS REGULATOR BCL-X


Mass: 17917.959 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-26,83-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07817
#2: Chemical ChemComp-X0D / (R)-2-(3-(3-((2,4-DIFLUOROPENYL)ETHYNYL)BENZOYL)-3-PROPYLUREIDO)-3-(ISOBUTYLTHIO) PROPANOIC ACID


Mass: 502.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H28F2N2O4S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 6.5
Details: 1.4 M (NH4)2SO4, 0.1 M MES PH 6.5, 25% (V/V) ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU / Date: Jan 11, 2008
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 20396 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 32.68 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 25
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.4 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MAZ

1maz


Resolution: 2.049→42.481 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 1038 5.1 %
Rwork0.159 --
obs0.1618 20291 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.6 Å2
Refinement stepCycle: LAST / Resolution: 2.049→42.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 153 133 2619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082547
X-RAY DIFFRACTIONf_angle_d1.1173430
X-RAY DIFFRACTIONf_dihedral_angle_d15.252890
X-RAY DIFFRACTIONf_chiral_restr0.068344
X-RAY DIFFRACTIONf_plane_restr0.005435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0492-2.15720.27261560.21732654X-RAY DIFFRACTION98
2.1572-2.29240.2451550.19122685X-RAY DIFFRACTION100
2.2924-2.46930.25461620.1692718X-RAY DIFFRACTION100
2.4693-2.71780.23851270.17332735X-RAY DIFFRACTION100
2.7178-3.1110.21281400.16132759X-RAY DIFFRACTION100
3.111-3.9190.19321590.14322772X-RAY DIFFRACTION100
3.919-42.49010.19871390.1472930X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.7021 Å / Origin y: -20.5544 Å / Origin z: -32.4289 Å
111213212223313233
T0.2127 Å2-0.0203 Å2-0.0129 Å2-0.2406 Å2-0.0127 Å2--0.291 Å2
L0.6563 °20.2186 °2-0.606 °2-0.4946 °2-0.2324 °2--2.0863 °2
S-0.0066 Å °0.0057 Å °-0.1063 Å °0.03 Å °-0.059 Å °-0.0281 Å °0.1015 Å °-0.068 Å °0.0703 Å °
Refinement TLS groupSelection details: ALL

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