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- PDB-4aq3: HUMAN BCL-2 WITH PHENYLACYLSULFONAMIDE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 4aq3
TitleHUMAN BCL-2 WITH PHENYLACYLSULFONAMIDE INHIBITOR
ComponentsAPOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1
KeywordsAPOPTOSIS / CHIMERA
Function / homology
Function and homology information


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 / channel inhibitor activity / melanin metabolic process ...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 / channel inhibitor activity / melanin metabolic process / positive regulation of neuron maturation / myeloid cell apoptotic process / cochlear nucleus development / osteoblast proliferation / mesenchymal cell development / retinal cell programmed cell death / negative regulation of osteoblast proliferation / stem cell development / gland morphogenesis / apoptotic process in bone marrow cell / renal system process / regulation of cell-matrix adhesion / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / negative regulation of calcium ion transport into cytosol / lymphoid progenitor cell differentiation / melanocyte differentiation / T cell apoptotic process / 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 / regulation of nitrogen utilization / glomerulus development / negative regulation of dendritic cell apoptotic process / focal adhesion assembly / regulation of transmembrane transporter activity / negative regulation of T cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / oocyte development / B cell apoptotic process / metanephros development / neuron maturation / negative regulation of motor neuron apoptotic process / Regulation of MITF-M-dependent genes involved in apoptosis / positive regulation of multicellular organism growth / regulation of viral genome replication / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / calcium ion transport into cytosol / negative regulation of ossification / response to UV-B / response to iron ion / negative regulation of mitochondrial depolarization / epithelial cell apoptotic process / Bcl-2 family protein complex / axon regeneration / motor neuron apoptotic process / positive regulation of smooth muscle cell migration / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of B cell apoptotic process / organ growth / hair follicle morphogenesis / branching involved in ureteric bud morphogenesis / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / B cell lineage commitment / hepatocyte apoptotic process / digestive tract morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of release of cytochrome c from mitochondria / pore complex / cellular response to alkaloid / negative regulation of intrinsic apoptotic signaling pathway / apoptotic mitochondrial changes / germ cell development / negative regulation of reproductive process / negative regulation of developmental process / T cell homeostasis / B cell homeostasis / BH3 domain binding / regulation of calcium ion transport / B cell proliferation / humoral immune response / negative regulation of anoikis / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / extrinsic apoptotic signaling pathway via death domain receptors / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria
Similarity search - Function
Apoptosis regulator, Bcl-2 / 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 / 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 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Chem-398 / Apoptosis regulator Bcl-2 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBertrand, J.A. / Fasolini, M. / Modugno, M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Identification of a Phenylacylsulfonamide Series of Dual Bcl-2/Bcl-Xl Antagonists.
Authors: Perez, H.L. / Banfi, P. / Bertrand, J.A. / Cai, Z.W. / Grebinski, J.W. / Kim, K. / Lippy, J. / Modugno, M. / Naglich, J. / Schmidt, R.J. / Tebben, A. / Vianello, P. / Wei, D.D. / Zhang, L. / ...Authors: Perez, H.L. / Banfi, P. / Bertrand, J.A. / Cai, Z.W. / Grebinski, J.W. / Kim, K. / Lippy, J. / Modugno, M. / Naglich, J. / Schmidt, R.J. / Tebben, A. / Vianello, P. / Wei, D.D. / Zhang, L. / Galvani, A. / Lombardo, L.J. / Borzilleri, R.M.
History
DepositionApr 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2May 1, 2024Group: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1
B: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1
C: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1
D: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1
E: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1
F: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,25512
Polymers117,0586
Non-polymers5,1976
Water00
1
A: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3762
Polymers19,5101
Non-polymers8661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3762
Polymers19,5101
Non-polymers8661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3762
Polymers19,5101
Non-polymers8661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3762
Polymers19,5101
Non-polymers8661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3762
Polymers19,5101
Non-polymers8661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3762
Polymers19,5101
Non-polymers8661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.214, 115.214, 102.318
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPTRPTRPAA10 - 3013 - 33
21ASPASPTRPTRPBB10 - 3013 - 33
31ASPASPTRPTRPCC10 - 3013 - 33
41ASPASPTRPTRPDD10 - 3013 - 33
51ASPASPTRPTRPEE10 - 3013 - 33
61ASPASPTRPTRPFF10 - 3013 - 33
12VALVALPHEPHEAA52 - 15755 - 160
22VALVALPHEPHEBB52 - 15755 - 160
32VALVALPHEPHECC52 - 15755 - 160
42VALVALPHEPHEDD52 - 15755 - 160
52VALVALPHEPHEEE52 - 15755 - 160
62VALVALPHEPHEFF52 - 15755 - 160

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999896, -0.002574, -0.014206), (0.00489, -0.986189, -0.165554), (-0.013583, -0.165606, 0.986098)-56.68136, 24.74994, 36.2198
3given(-0.501065, 0.860651, -0.090629), (-0.833152, -0.508062, -0.218473), (-0.234074, -0.033961, 0.971625)-0.46102, -5.25083, -1.35637
4given(0.998112, -0.011743, 0.06029), (0.011612, 0.999929, 0.002517), (-0.060316, -0.001812, 0.998178)-0.82415, -1.77654, 33.11996
5given(-0.999594, -0.006045, 0.027859), (0.002596, -0.992501, -0.122213), (0.028389, -0.122091, 0.992113)-59.37437, 28.60782, 2.53127
6given(0.477377, -0.870284, 0.121313), (0.870083, 0.487455, 0.073092), (-0.122745, 0.07066, 0.98992)54.98487, 34.36977, -11.18358

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Components

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


Mass: 19509.666 Da / Num. of mol.: 6
Fragment: RESIDUES 1-33 AND 92-207 OF P10415 AND RESIDUES 29-44 OF Q07817
Source method: isolated from a genetically manipulated source
Details: APOPTOSIS REGULATOR BCL-2 WITH PUTATIVE FLEXIBLE LOOP REPLACED WITH A PORTION OF APOPTOSIS REGULATOR BCL-X PROTEIN
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P10415, UniProt: Q07817
#2: Chemical
ChemComp-398 / N,N-dibutyl-4-chloranyl-1-[2-(3,4-dihydro-1H-isoquinolin-2-ylcarbonyl)-4-[(7-iodanylnaphthalen-2-yl)sulfonylcarbamoyl]phenyl]-5-methyl-pyrazole-3-carboxamide


Mass: 866.207 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H41ClIN5O5S

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 58071 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.8 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INTERNAL STRUCTURE

Resolution: 2.4→100 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.963 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24494 2926 5 %RANDOM
Rwork0.20072 ---
obs0.203 55094 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.235 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6778 0 318 0 7096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197311
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9619916
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.875802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70522.581403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.747151108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3731572
X-RAY DIFFRACTIONr_chiral_restr0.1110.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025854
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1059 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.320.5
2Bmedium positional0.270.5
3Cmedium positional0.350.5
4Dmedium positional0.320.5
5Emedium positional0.340.5
6Fmedium positional0.340.5
1Amedium thermal5.652
2Bmedium thermal4.562
3Cmedium thermal5.892
4Dmedium thermal5.632
5Emedium thermal6.72
6Fmedium thermal6.012
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 174 -
Rwork0.317 3637 -
obs--87.19 %
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)
12.2077-0.25390.55961.52790.17091.249-0.0469-0.00350.167-0.0266-0.04630.0156-0.09030.04460.09320.08790.01780.00180.0672-0.02280.0304-13.890214.216-10.2099
22.1553-0.5062-0.32551.36960.42851.4854-0.08570.0387-0.05720.1530.0795-0.00990.09780.02410.00620.09520.03920.02410.04970.03160.0425-42.21217.9809-44.6444
30.64810.0372-0.03883.12350.57441.55240.10680.0135-0.0601-0.0108-0.15550.10840.081-0.16440.04870.0892-0.01710.00520.0697-0.00710.0204-7.4064-21.1416-11.637
43.3229-1.57190.53861.5146-0.04272.2469-0.19760.31950.33110.0809-0.00810.0013-0.17980.15130.20570.0482-0.017-0.05650.06780.04050.1338-10.350216.4464-44.0337
54.7431-1.4547-0.65131.74090.58651.5761-0.27770.1166-0.3711-0.01970.14020.36790.09170.09480.13750.05030.00040.01820.04580.04260.0997-45.94315.6412-9.4843
61.5204-0.67440.52222.29720.18251.26140.10090.15690.1134-0.1511-0.1342-0.1282-0.02210.15210.03330.0554-0.0098-0.00190.05340.04710.0843-50.392450.2935-8.9127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 166
2X-RAY DIFFRACTION2B-2 - 166
3X-RAY DIFFRACTION3C-2 - 166
4X-RAY DIFFRACTION4D-2 - 166
5X-RAY DIFFRACTION5E-2 - 166
6X-RAY DIFFRACTION6F-2 - 166

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