[English] 日本語
Yorodumi
- PDB-4kba: CK1d in complex with 9-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kba
TitleCK1d in complex with 9-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]-2,3,4,5-tetrahydropyrido[2,3-f][1,4]oxazepine inhibitor
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ser/thr kinase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / midbrain dopaminergic neuron differentiation / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport ...positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / midbrain dopaminergic neuron differentiation / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport / tau-protein kinase activity / Golgi organization / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / AURKA Activation by TPX2 / cellular response to nerve growth factor stimulus / ciliary basal body / spindle microtubule / circadian regulation of gene expression / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / positive regulation of canonical Wnt signaling pathway / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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-1QM / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLiu, S.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Ligand-protein interactions of selective casein kinase 1 delta inhibitors.
Authors: Mente, S. / Arnold, E. / Butler, T. / Chakrapani, S. / Chandrasekaran, R. / Cherry, K. / Dirico, K. / Doran, A. / Fisher, K. / Galatsis, P. / Green, M. / Hayward, M. / Humphrey, J. / ...Authors: Mente, S. / Arnold, E. / Butler, T. / Chakrapani, S. / Chandrasekaran, R. / Cherry, K. / Dirico, K. / Doran, A. / Fisher, K. / Galatsis, P. / Green, M. / Hayward, M. / Humphrey, J. / Knafels, J. / Li, J. / Liu, S. / Marconi, M. / McDonald, S. / Ohren, J. / Paradis, V. / Sneed, B. / Walton, K. / Wager, T.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Casein kinase I isoform delta
B: Casein kinase I isoform delta
C: Casein kinase I isoform delta
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,31117
Polymers154,1494
Non-polymers2,16213
Water3,171176
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0544
Polymers38,5371
Non-polymers5163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0544
Polymers38,5371
Non-polymers5163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0544
Polymers38,5371
Non-polymers5163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1505
Polymers38,5371
Non-polymers6134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Casein kinase I isoform delta
hetero molecules

B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1078
Polymers77,0742
Non-polymers1,0336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3060 Å2
ΔGint-67 kcal/mol
Surface area24070 Å2
MethodPISA
6
D: Casein kinase I isoform delta
hetero molecules

C: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2039
Polymers77,0742
Non-polymers1,1297
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area3290 Å2
ΔGint-77 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.689, 83.964, 89.290
Angle α, β, γ (deg.)108.00, 105.71, 93.00
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Casein kinase I isoform delta / CKI-delta / CKId / Tau-protein kinase CSNK1D


Mass: 38537.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical
ChemComp-1QM / 9-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]-2,3,4,5-tetrahydropyrido[2,3-f][1,4]oxazepine


Mass: 324.352 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H17FN4O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.63 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→80.95 Å / Num. all: 95216 / Num. obs: 85686 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 23.34 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 6.9

-
Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→19.96 Å / Cor.coef. Fo:Fc: 0.9164 / Cor.coef. Fo:Fc free: 0.889 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 4379 5.12 %RANDOM
Rwork0.2084 ---
obs0.2099 85598 96.09 %-
Displacement parametersBiso mean: 35.53 Å2
Baniso -1Baniso -2Baniso -3
1--2.2783 Å22.3569 Å2-0.3522 Å2
2--1.2224 Å2-2.5499 Å2
3---1.0559 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: LAST / Resolution: 1.98→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8948 0 141 176 9265
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019375HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0312663HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3318SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes200HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1460HARMONIC5
X-RAY DIFFRACTIONt_it9375HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion19.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1119SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10501SEMIHARMONIC4
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2412 300 4.95 %
Rwork0.2017 5766 -
all0.2036 6066 -
obs--96.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35370.3266-0.24860.4488-0.13551.54090.049-0.08160.055-0.04660.03780.081-0.1014-0.1127-0.0868-0.13130.07760.06950.26730.1714-0.1210.0296-0.63030.9696
20.80110.1373-0.37240.7185-0.94042.29190.0355-0.120.03340.0959-0.04460.023-0.35530.32630.009-0.0416-0.0360.05520.24190.1141-0.161117.687416.7904-37.7309
31.6459-0.33640.2590.28670.01971.5680.06150.0435-0.06870.06280.04170.07410.0945-0.18-0.1031-0.09740.0451-0.00830.22110.1637-0.1372-0.4596-22.8877-41.1461
40.878-0.18470.20280.6241-0.82382.1290.02630.0857-0.0353-0.0853-0.02530.0330.29550.3183-0.001-0.03220.1413-0.01740.25940.1296-0.17417.1413-39.1352-2.8801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|293 A|401 - A|401 }A3 - 293
2X-RAY DIFFRACTION1{ A|3 - A|293 A|401 - A|401 }A401
3X-RAY DIFFRACTION2{ B|3 - B|293 B|401 - B|401 }B3 - 293
4X-RAY DIFFRACTION2{ B|3 - B|293 B|401 - B|401 }B401
5X-RAY DIFFRACTION3{ C|7 - C|293 C|401 - C|401 }C7 - 293
6X-RAY DIFFRACTION3{ C|7 - C|293 C|401 - C|401 }C401
7X-RAY DIFFRACTION4{ D|3 - D|293 D|401 - D|401 }D3 - 293
8X-RAY DIFFRACTION4{ D|3 - D|293 D|401 - D|401 }D401

+
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