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- PDB-8fbv: Compound 7 bound to procaspase-6 -

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Basic information

Entry
Database: PDB / ID: 8fbv
TitleCompound 7 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 / cellular response to staurosporine / positive regulation of necroptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / Apoptotic cleavage of cellular proteins / 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 / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / Apoptotic cleavage of cellular proteins / 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 / cytosol / cytoplasm
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-XOW / Caspase-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 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 30, 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)137,0566
Polymers136,4874
Non-polymers5692
Water1,67593
1
A: Procaspase-6
B: Procaspase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5283
Polymers68,2442
Non-polymers2841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-15 kcal/mol
Surface area21290 Å2
MethodPISA
2
C: Procaspase-6
D: Procaspase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5283
Polymers68,2442
Non-polymers2841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-19 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.570, 101.570, 321.260
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-XOW / 5-fluoro-2-({[(3M)-3-(1H-imidazol-2-yl)pyridin-2-yl]amino}methyl)phenol


Mass: 284.288 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13FN4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.5 Å3/Da / Density % sol: 64.91 %
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: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 2.85→48.42 Å / Num. obs: 26346 / % possible obs: 60.8 % / Redundancy: 15.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.052 / Rrim(I) all: 0.202 / Χ2: 0.99 / Net I/σ(I): 11.9 / Num. measured all: 402198
Reflection shellResolution: 2.85→3.01 Å / % possible obs: 4.5 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.683 / Num. measured all: 2895 / Num. unique obs: 284 / CC1/2: 0.95 / Rpim(I) all: 0.223 / Rrim(I) all: 0.719 / Χ2: 0.91 / Net I/σ(I) obs: 3.3

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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: 2.86→48.42 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.892 / SU B: 6.793 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22086 1333 5.1 %RANDOM
Rwork0.18891 ---
obs0.19047 25010 60.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.223 Å2
Baniso -1Baniso -2Baniso -3
1-8.17 Å20 Å20 Å2
2--8.17 Å20 Å2
3----16.33 Å2
Refinement stepCycle: 1 / Resolution: 2.86→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7925 0 42 93 8060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138199
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157640
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.65611040
X-RAY DIFFRACTIONr_angle_other_deg1.1731.59217585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8085978
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98421.581449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.678151425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.61556
X-RAY DIFFRACTIONr_chiral_restr0.0520.21026
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029213
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022015
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_it2.674.0763936
X-RAY DIFFRACTIONr_mcbond_other2.6614.0753935
X-RAY DIFFRACTIONr_mcangle_it4.5526.0864906
X-RAY DIFFRACTIONr_mcangle_other4.5526.0874907
X-RAY DIFFRACTIONr_scbond_it2.7484.5184263
X-RAY DIFFRACTIONr_scbond_other2.7484.5184264
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8336.6296135
X-RAY DIFFRACTIONr_long_range_B_refined7.72545.3248746
X-RAY DIFFRACTIONr_long_range_B_other7.72145.3478735
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)
11A79980.04
12B79980.04
21A76870.08
22C76870.08
31A77730.07
32D77730.07
41B77580.07
42C77580.07
51B77740.07
52D77740.07
61C78670.07
62D78670.07
LS refinement shellResolution: 2.86→2.932 Å
RfactorNum. reflection% reflection
Rfree0.434 2 -
Rwork0.216 79 -
obs--2.56 %

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