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- PDB-3zlo: Crystal structure of BCL-XL in complex with inhibitor (Compound 6) -

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Basic information

Entry
Database: PDB / ID: 3zlo
TitleCrystal structure of BCL-XL in complex with inhibitor (Compound 6)
ComponentsBCL-2-LIKE PROTEIN 1
KeywordsAPOPTOSIS / INHIBITOR
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-X8U / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsCzabotar, P.E. / Lessene, G.L. / Smith, B.J. / Colman, P.M.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Structure-Guided Design of a Selective Bcl-Xl Inhibitor
Authors: Lessene, G.L. / Czabotar, P.E. / Sleebs, B.E. / Zobel, K. / Lowes, K.L. / Adams, J.M. / Baell, J.B. / Colman, P.M. / Deshayes, K. / Fairbrother, W.J. / Flygare, J.A. / Gibbons, P. / Kersten, ...Authors: Lessene, G.L. / Czabotar, P.E. / Sleebs, B.E. / Zobel, K. / Lowes, K.L. / Adams, J.M. / Baell, J.B. / Colman, P.M. / Deshayes, K. / Fairbrother, W.J. / Flygare, J.A. / Gibbons, P. / Kersten, W.J.A. / Kulasegaram, S. / Moss, R.M. / Parisot, J.P. / Smith, B.J. / Street, I.P. / Yang, H. / Huang, D.C.S. / Watson, K.G.
History
DepositionFeb 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Jun 13, 2018Group: Data collection / Database references / Structure summary
Category: citation / struct / Item: _citation.page_last / _struct.title
Revision 1.4Dec 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,3582
Polymers20,8051
Non-polymers5531
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.832, 67.832, 67.383
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 20804.918 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-44 AND 85-209
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-X8U / 2-[(8E)-8-(1,3-benzothiazol-2-ylhydrazinylidene)-6,7-dihydro-5H-naphthalen-2-yl]-5-(4-phenylbutyl)-1,3-thiazole-4-carboxylic acid


Mass: 552.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H28N4O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 45 TO 84 REMOVED, LAST 25 RESIDUES TRUNCATED

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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: 2.15 Å3/Da / Density % sol: 47.76 % / Description: NONE
Crystal growpH: 6
Details: 2 M (NH4)2SO4, 0.5 M GUANADINE HCL, 0.1 M MES PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS-IV / Detector: IMAGE PLATE / Date: Sep 3, 2007 / Details: MEECO CAPILLARY
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 5766 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 0
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZK6 CHAIN A

3zk6


Resolution: 2.601→33.916 Å / SU ML: 0.4 / σ(F): 1.38 / Phase error: 31.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2822 265 4.6 %
Rwork0.1932 --
obs0.1972 5766 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.601→33.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 0 39 6 1187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091213
X-RAY DIFFRACTIONf_angle_d1.1881644
X-RAY DIFFRACTIONf_dihedral_angle_d13.438425
X-RAY DIFFRACTIONf_chiral_restr0.069167
X-RAY DIFFRACTIONf_plane_restr0.005211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6011-3.27670.35171370.25172678X-RAY DIFFRACTION100
3.2767-33.91890.2631280.17852823X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5959-1.86560.43017.13772.49988.29210.460.45060.576-0.469-0.0115-0.345-2.82941.155-0.5120.5798-0.20620.13480.68670.04880.803424.3098-17.99810.2882
22.9739-2.2725-3.22472.55781.71974.0768-0.2396-0.73911.15320.51140.11190.10420.48221.94920.05830.6871-0.3736-0.09261.3133-0.28680.782830.0062-17.984817.8025
33.85863.8601-3.98333.8372-3.94714.08280.73020.17180.3180.5840.21060.6081-0.8885-0.8075-0.55360.66140.09440.13330.73180.05620.64114.4693-19.344914.0264
44.178-5.8020.67798.83520.58753.8514-1.6024-0.4176-0.84570.62491.01270.08891.8955-0.56960.62311.0021-0.03580.11380.85880.19550.899718.0004-36.683214.0215
59.23070.9945-2.18186.8934-0.67386.86180.21660.7933-0.3833-0.6174-0.0737-0.28711.40290.6151-0.08430.50280.02610.05310.7416-0.00160.429626.3342-30.23016.6523
64.63420.55184.14237.3531-2.17845.2846-0.36333.48071.4744-1.25170.04950.8141-1.2525-0.85530.47980.67270.1713-0.09661.73290.53541.012914.227-21.7159-4.4669
71.87960.09030.10190.73280.85590.99770.0264-0.0752-0.23050.44270.7520.6079-0.3658-1.44361.5520.37810.3878-0.08431.670.72811.2539.2178-16.82594.7468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:19)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 20:81)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 82:100)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 101:111)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 112:177)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 178:186)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 187:196)

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