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- PDB-3zk6: Crystal structure of Bcl-xL in complex with inhibitor (Compound 2). -

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Basic information

Entry
Database: PDB / ID: 3zk6
TitleCrystal structure of Bcl-xL in complex with inhibitor (Compound 2).
ComponentsBCL-2-LIKE PROTEIN 1
KeywordsAPOPTOSIS / INHIBITOR / BCL-2 FAMILY
Function / homology
Function and homology information


apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / 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 ...apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / 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 / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / cytoplasm / cytosol
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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Chem-H1I / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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
DepositionJan 22, 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 1.3Dec 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)42,7164
Polymers41,5422
Non-polymers1,1732
Water97354
1
A: BCL-2-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3582
Polymers20,7711
Non-polymers5871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BCL-2-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3582
Polymers20,7711
Non-polymers5871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.200, 65.200, 117.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B

NCS oper: (Code: given
Matrix: (-0.001619, 0.999994, 0.003115), (0.999999, 0.001621, -0.000549), (-0.000554, 0.003115, -0.999995)
Vector: -32.562, 32.5202, 0.07304)

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Components

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


Mass: 20771.055 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-40 AND 81-209
Source method: isolated from a genetically manipulated source
Details: DELETION MUTATION PERFORMED. TRUNCATION REMOVES RESIDUES 41-80, AND 210-233
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q07817
#2: Chemical ChemComp-H1I / N-(3-(5-(1-(2-(benzo[d]thiazol-2-yl)hydrazono)ethyl)furan-2-yl)phenylsulfonyl)-6-phenylhexanamide


Mass: 586.724 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H30N4O4S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 41 TO 80 REMOVED, LAST 24 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: 3 Å3/Da / Density % sol: 59.96 % / Description: NONE
Crystal growDetails: 2.2 M (NH4)2 SO4, 0.1 M BIS TRIS, PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.96426
DetectorDate: Jun 20, 2006
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96426 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.49
ReflectionResolution: 2.48→46.1 Å / Num. obs: 17277 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.45 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.62
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 7.14 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.58 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PQ1 CHAIN A.

1pq1


Resolution: 2.48→46.103 Å / σ(F): 2 / Phase error: 27.3 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2607 871 5 %
Rwork0.2214 --
obs0.2215 17274 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→46.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 82 54 2470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082482
X-RAY DIFFRACTIONf_angle_d1.3123362
X-RAY DIFFRACTIONf_dihedral_angle_d19.667862
X-RAY DIFFRACTIONf_chiral_restr0.082340
X-RAY DIFFRACTIONf_plane_restr0.005428
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1167X-RAY DIFFRACTIONPOSITIONAL
12B1167X-RAY DIFFRACTIONPOSITIONAL0.042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4807-2.63610.34921410.26592647X-RAY DIFFRACTION92
2.6361-2.83950.31981440.24852739X-RAY DIFFRACTION95
2.8395-3.12490.25051460.23422741X-RAY DIFFRACTION95
3.1249-3.57640.27971440.22212741X-RAY DIFFRACTION95
3.5764-4.50320.23481440.20052737X-RAY DIFFRACTION95
4.5032-29.16030.24641470.2122788X-RAY DIFFRACTION95
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)
16.60552.6955-2.15266.434-0.10092.5457-0.50710.5923-0.9946-0.42930.3562-0.8729-0.09590.214-0.05220.59250.02960.11640.5994-0.15310.196132.202337.2013-9.7401
28.28920.95271.03286.9331-0.5075.13990.0879-0.10040.32570.46670.496-0.4632-1.18280.5301-0.50250.6747-0.1447-0.03060.7311-0.0480.283932.432449.3173.6748
34.4595-0.14940.70743.95740.32712.8687-0.39780.03290.1149-0.16050.5902-0.3463-0.41640.3309-0.21260.507-0.06090.03380.6937-0.02280.259736.824442.8651-1.3703
41.86971.27051.14695.01563.17698.14330.07370.27350.0373-0.2998-0.07460.10050.2677-0.07060.13180.5142-0.0206-0.06770.8260.0920.178520.797532.22910.9068
53.5621.87060.2435.88733.13797.70060.2069-0.45640.2345-0.2689-0.24860.3384-0.5952-0.21010.24330.681-0.0041-0.0620.5479-0.00420.26044.581564.740610.0124
64.6371.4613-0.08077.473-1.53086.91740.13170.24060.5346-0.47340.14430.0715-0.88050.6862-0.38410.68930.20760.08450.5163-0.05460.288716.688865.0325-3.4082
75.68011.02191.39585.8767-0.27672.5532-0.22870.27281.0006-0.07480.04250.2406-0.47820.04060.04910.75610.20380.04950.36930.02470.33510.23569.39781.6526
89.55512.7939-4.96052.8596-2.53373.5778-0.825-0.1499-0.22670.3169-0.1718-0.00570.4515-0.52740.58520.74990.1685-0.13710.4428-0.08960.3618-0.378753.3632-0.6668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:100)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 101:136)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 137:177)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 178:196)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 2:100)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 101:136)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 137:177)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 178:196)

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