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- PDB-8f78: Compound 1 bound to procaspase-6 -

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Basic information

Entry
Database: PDB / ID: 8f78
TitleCompound 1 bound to procaspase-6
ComponentsProcaspase-6
KeywordsAPOPTOSIS / inhibitor / procaspase-6 / protease
Function / homology
Function and homology information


caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / cellular response to staurosporine / positive regulation of necroptotic process / Apoptotic cleavage of cellular proteins / TP53 Regulates Transcription of Caspase Activators and Caspases / hepatocyte apoptotic process / pyroptotic inflammatory response / protein autoprocessing ...caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / cellular response to staurosporine / positive regulation of necroptotic process / Apoptotic cleavage of cellular proteins / TP53 Regulates Transcription of Caspase Activators and Caspases / hepatocyte apoptotic process / pyroptotic inflammatory response / protein autoprocessing / intrinsic apoptotic signaling pathway by p53 class mediator / Caspase-mediated cleavage of cytoskeletal proteins / epithelial cell differentiation / cysteine-type peptidase activity / activation of innate immune response / positive regulation of neuron apoptotic process / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / proteolysis / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain ...Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily
Similarity search - Domain/homology
Chem-2J6 / Caspase-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsFan, P. / Zhao, Y. / Renslo, A.R. / Arkin, M.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Systematic Study of Heteroarene Stacking Using a Congeneric Set of Molecular Glues for Procaspase-6.
Authors: Togo, T. / Tram, L. / Denton, L.G. / ElHilali-Pollard, X. / Gu, J. / Jiang, J. / Liu, C. / Zhao, Y. / Zhao, Y. / Zheng, Y. / Zheng, Y. / Yang, J. / Fan, P. / Arkin, M.R. / Harma, H. / Sun, D. ...Authors: Togo, T. / Tram, L. / Denton, L.G. / ElHilali-Pollard, X. / Gu, J. / Jiang, J. / Liu, C. / Zhao, Y. / Zhao, Y. / Zheng, Y. / Zheng, Y. / Yang, J. / Fan, P. / Arkin, M.R. / Harma, H. / Sun, D. / Canan, S.S. / Wheeler, S.E. / Renslo, A.R.
History
DepositionNov 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Procaspase-6
B: Procaspase-6
C: Procaspase-6
D: Procaspase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,22210
Polymers136,4874
Non-polymers7346
Water3,261181
1
A: Procaspase-6
B: Procaspase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5754
Polymers68,2442
Non-polymers3322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-25 kcal/mol
Surface area21330 Å2
MethodPISA
2
C: Procaspase-6
D: Procaspase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6466
Polymers68,2442
Non-polymers4034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-51 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.277, 102.277, 321.648
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Procaspase-6 / CASP-6 / CSP-6 / Apoptotic protease Mch-2


Mass: 34121.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6, MCH2 / Production host: Escherichia coli (E. coli) / References: UniProt: P55212, caspase-6
#2: Chemical ChemComp-2J6 / 5-fluoro-2-({[3-(pyrimidin-2-yl)pyridin-2-yl]amino}methyl)phenol


Mass: 296.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13FN4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.56 Å3/Da / Density % sol: 65.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7; 8% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.65→85.4 Å / Num. obs: 53836 / % possible obs: 97.7 % / Redundancy: 19.8 % / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.013 / Rrim(I) all: 0.058 / Χ2: 1 / Net I/σ(I): 31.3 / Num. measured all: 1066294
Reflection shellResolution: 2.65→2.73 Å / % possible obs: 84.6 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.593 / Num. measured all: 54101 / Num. unique obs: 4028 / CC1/2: 0.977 / Rpim(I) all: 0.162 / Rrim(I) all: 0.616 / Χ2: 1.01 / Net I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→85.4 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 6.728 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20662 2751 5.1 %RANDOM
Rwork0.16408 ---
obs0.16621 50980 97.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.008 Å2
Baniso -1Baniso -2Baniso -3
1-49.4 Å20 Å20 Å2
2--49.4 Å20 Å2
3----98.8 Å2
Refinement stepCycle: 1 / Resolution: 2.65→85.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8008 0 48 181 8237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138301
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157725
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.65611179
X-RAY DIFFRACTIONr_angle_other_deg1.1781.59117783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1815991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.4621.645456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.562151444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0931556
X-RAY DIFFRACTIONr_chiral_restr0.0530.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029335
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022041
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_it5.1187.9223976
X-RAY DIFFRACTIONr_mcbond_other5.1087.9213975
X-RAY DIFFRACTIONr_mcangle_it7.53311.8684957
X-RAY DIFFRACTIONr_mcangle_other7.53411.8714958
X-RAY DIFFRACTIONr_scbond_it5.1118.3454325
X-RAY DIFFRACTIONr_scbond_other5.118.3444326
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.66512.3546221
X-RAY DIFFRACTIONr_long_range_B_refined11.13789.3298967
X-RAY DIFFRACTIONr_long_range_B_other11.13489.3258949
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 177 -
Rwork0.235 3207 -
obs--83.33 %

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