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- PDB-8f9d: Compound 21 bound to procaspase-6 -

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Basic information

Entry
Database: PDB / ID: 8f9d
TitleCompound 21 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
DI(HYDROXYETHYL)ETHER / Chem-XNK / 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 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)137,4669
Polymers136,4874
Non-polymers9795
Water3,387188
1
A: Procaspase-6
B: Procaspase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5303
Polymers68,2442
Non-polymers2861
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-17 kcal/mol
Surface area21680 Å2
MethodPISA
2
C: Procaspase-6
D: Procaspase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9366
Polymers68,2442
Non-polymers6934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-15 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.529, 101.529, 321.926
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

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 193 molecules

#2: Chemical ChemComp-XNK / 5-fluoro-2-({[(3M)-3-(1,2,4-oxadiazol-3-yl)pyridin-2-yl]amino}methyl)phenol


Mass: 286.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11FN4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.51 Å3/Da / Density % sol: 64.95 %
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: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.65→48.41 Å / Num. obs: 54317 / % possible obs: 99.9 % / Redundancy: 15.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.04 / Rrim(I) all: 0.159 / Χ2: 1 / Net I/σ(I): 15.2 / Num. measured all: 852492
Reflection shellResolution: 2.65→2.73 Å / % possible obs: 100 % / Redundancy: 16.2 % / Rmerge(I) obs: 1.685 / Num. measured all: 72174 / Num. unique obs: 4446 / CC1/2: 0.886 / Rpim(I) all: 0.431 / Rrim(I) all: 1.74 / Χ2: 0.98 / Net I/σ(I) obs: 1.8

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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→48.46 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 12.906 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 2769 5.1 %RANDOM
Rwork0.19327 ---
obs0.1951 51447 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.876 Å2
Baniso -1Baniso -2Baniso -3
1-3.3 Å21.65 Å20 Å2
2--3.3 Å2-0 Å2
3----10.7 Å2
Refinement stepCycle: 1 / Resolution: 2.65→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7974 0 69 188 8231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138286
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157725
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.65611148
X-RAY DIFFRACTIONr_angle_other_deg1.2741.5917788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6535987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.74821.611453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.933151439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2751556
X-RAY DIFFRACTIONr_chiral_restr0.0680.21033
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022025
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_it5.5457.2683960
X-RAY DIFFRACTIONr_mcbond_other5.5397.2673959
X-RAY DIFFRACTIONr_mcangle_it8.11510.8884937
X-RAY DIFFRACTIONr_mcangle_other8.11610.894938
X-RAY DIFFRACTIONr_scbond_it6.4197.9954326
X-RAY DIFFRACTIONr_scbond_other6.4197.9964327
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.711.7236210
X-RAY DIFFRACTIONr_long_range_B_refined11.91180.518676
X-RAY DIFFRACTIONr_long_range_B_other11.91680.5018662
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)
11A81800.04
12B81800.04
21A77650.08
22C77650.08
31A78490.06
32D78490.06
41B77780.07
42C77780.07
51B78550.06
52D78550.06
61C78260.06
62D78260.06
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 203 -
Rwork0.401 3816 -
obs--99.85 %

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