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- PDB-8f96: Compound 3 bound to procaspase-6 -

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Basic information

Entry
Database: PDB / ID: 8f96
TitleCompound 3 bound to procaspase-6
ComponentsProcaspase-6
KeywordsAPOPTOSIS / HYDROLASE/INHIBITOR / inhibitor / procaspase-6 / protease / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / : / : / TP53 Regulates Transcription of Caspase Activators and Caspases / hepatocyte apoptotic process / Apoptotic cleavage of cellular proteins ...caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / : / : / TP53 Regulates Transcription of Caspase Activators and Caspases / hepatocyte apoptotic process / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / intrinsic apoptotic signaling pathway by p53 class mediator / protein autoprocessing / Caspase-mediated cleavage of cytoskeletal proteins / cysteine-type peptidase activity / epithelial cell differentiation / 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 / cytosol / cytoplasm
Similarity search - Function
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. ...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-XLW / Caspase-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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 23, 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)137,0806
Polymers136,4874
Non-polymers5932
Water1,72996
1
A: Procaspase-6
B: Procaspase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5403
Polymers68,2442
Non-polymers2961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-19 kcal/mol
Surface area20950 Å2
MethodPISA
2
C: Procaspase-6
D: Procaspase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5403
Polymers68,2442
Non-polymers2961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-17 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.333, 101.333, 321.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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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-XLW / 5-fluoro-2-({[(3M)-3-(pyrimidin-4-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.49 Å3/Da / Density % sol: 64.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7, 4% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→45.93 Å / Num. obs: 39151 / % possible obs: 99.8 % / Redundancy: 9.6 % / CC1/2: 0.979 / Rmerge(I) obs: 0.283 / Rpim(I) all: 0.084 / Rrim(I) all: 0.297 / Χ2: 0.99 / Net I/σ(I): 5.5 / Num. measured all: 375269
Reflection shellResolution: 2.95→3.07 Å / % possible obs: 99.8 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.793 / Num. measured all: 43022 / Num. unique obs: 4457 / CC1/2: 0.909 / Rpim(I) all: 0.239 / Rrim(I) all: 0.832 / Χ2: 1.04 / Net I/σ(I) obs: 1.9

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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: 2.95→45.85 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 16.967 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.775 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22739 2044 5.2 %RANDOM
Rwork0.19559 ---
obs0.19724 37016 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.922 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å21.53 Å20 Å2
2--3.05 Å2-0 Å2
3----9.89 Å2
Refinement stepCycle: 1 / Resolution: 2.95→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7907 0 44 96 8047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138185
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157624
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.65711020
X-RAY DIFFRACTIONr_angle_other_deg1.2481.59217549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7175976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39521.544447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.645151421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9051556
X-RAY DIFFRACTIONr_chiral_restr0.0630.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022009
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_it5.3057.1183928
X-RAY DIFFRACTIONr_mcbond_other5.37.1163927
X-RAY DIFFRACTIONr_mcangle_it7.94910.6674896
X-RAY DIFFRACTIONr_mcangle_other7.9510.6694897
X-RAY DIFFRACTIONr_scbond_it6.0047.7564257
X-RAY DIFFRACTIONr_scbond_other6.0047.7574258
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.17711.4036125
X-RAY DIFFRACTIONr_long_range_B_refined11.66479.0528603
X-RAY DIFFRACTIONr_long_range_B_other11.67279.0628600
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A78510.06
12B78510.06
21A76970.07
22C76970.07
31A77730.08
32D77730.08
41B77040.07
42C77040.07
51B77370.07
52D77370.07
61C79330.04
62D79330.04
LS refinement shellResolution: 2.95→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 160 -
Rwork0.349 2704 -
obs--99.72 %

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