[English] 日本語
Yorodumi
- PDB-2pvh: Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivati... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pvh
TitleStructure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Structure-Based Drug Design / Enzyme-Inhibitor Complex / Casein Kinase II / Protein Kinase CK2
Function / homology
Function and homology information


protein kinase CK2 complex / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity ...protein kinase CK2 complex / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / Rho-dependent protein serine/threonine kinase activity / ribosomal protein S6 kinase activity / histone H2BS14 kinase activity / histone H3T6 kinase activity / histone H3T45 kinase activity / histone H3S10 kinase activity / histone H3T11 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / regulation of cell cycle / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / protein serine kinase activity / DNA damage response / ATP binding / nucleus / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-P19 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsNie, Z. / Perretta, C. / Erickson, P. / Margosiak, S. / Almassy, R. / Lu, J. / Averill, A. / Yager, K.M. / Chu, S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Structure-based design, synthesis, and study of pyrazolo[1,5-a][1,3,5]triazine derivatives as potent inhibitors of protein kinase CK2.
Authors: Nie, Z. / Perretta, C. / Erickson, P. / Margosiak, S. / Almassy, R. / Lu, J. / Averill, A. / Yager, K.M. / Chu, S.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7532
Polymers41,4501
Non-polymers3021
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.294, 59.274, 44.943
Angle α, β, γ (deg.)90.00, 102.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-659-

HOH

-
Components

#1: Protein Casein kinase II subunit alpha / CK II / CK2-alpha / Protein kinase CK2 alpha


Mass: 41450.465 Da / Num. of mol.: 1 / Mutation: V256A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ACK2 / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-P19 / N,N'-DIPHENYLPYRAZOLO[1,5-A][1,3,5]TRIAZINE-2,4-DIAMINE


Mass: 302.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% PEG 4000, 0.20M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 107 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 10, 2005 / Details: MIRRORS
RadiationMonochromator: OSMIC CONFOCAL MAX-FLUX MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 18543 / Num. obs: 18543 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.059 / Χ2: 0.956 / Net I/σ(I): 21.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1796 / Χ2: 1.075 / % possible all: 97.4

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
DENZOdata reduction
CNXphasing
CNXrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1OM1 PROTEIN MODEL

1om1


Resolution: 2.2→50 Å / FOM work R set: 0.847 / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1767 -RANDOM
Rwork0.192 ---
all0.196 18005 --
obs0.196 18005 100 %-
Displacement parametersBiso mean: 32.24 Å2
Baniso -1Baniso -2Baniso -3
1-8.933 Å20 Å22.149 Å2
2---11.559 Å20 Å2
3---2.627 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.321 Å0.249 Å
Luzzati d res low-5 Å
Luzzati sigma a0.303 Å0.226 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 23 161 2918
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_dihedral_angle_d20.91
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it2.992.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 35

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.2-2.220.395320.313333365
2.22-2.240.37610.269464525
2.24-2.270.37410.264402443
2.27-2.290.244380.25428466
2.29-2.320.243510.213428479
2.32-2.340.321510.25456507
2.34-2.370.286500.205467517
2.37-2.40.277440.2442486
2.4-2.430.288450.194450495
2.43-2.460.215540.185465519
2.46-2.490.273400.202496536
2.49-2.530.297370.193455492
2.53-2.570.253510.189468519
2.57-2.610.29540.205449503
2.61-2.650.284460.218490536
2.65-2.70.296530.243450503
2.7-2.750.288610.205437498
2.75-2.80.239610.185474535
2.8-2.860.264420.201499541
2.86-2.920.269610.204442503
2.92-2.990.257590.201489548
2.99-3.060.24430.19455498
3.06-3.140.242490.209485534
3.14-3.240.242540.186490544
3.24-3.340.255550.207455510
3.34-3.460.256570.202482539
3.46-3.60.276490.2476525
3.6-3.760.268460.194501547
3.76-3.960.192490.177473522
3.96-4.210.193510.155497548
4.21-4.530.162600.148477537
4.53-4.990.151430.14501544
4.99-5.710.221590.196475534
5.71-7.20.213620.205483545
7.2-500.010.178580.173504562

+
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