[English] 日本語
Yorodumi
- PDB-8f78: Compound 1 bound to procaspase-6 -

+
Open data


ID or keywords:

Loading...

-
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 / 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-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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more