[English] 日本語
Yorodumi
- PDB-3kvx: JNK3 bound to aminopyrimidine inhibitor, SR-3562 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kvx
TitleJNK3 bound to aminopyrimidine inhibitor, SR-3562
ComponentsMitogen-activated protein kinase 10
KeywordsTRANSFERASE / JNK3 / MAPK10 / inhibitor / ATP-binding / Epilepsy / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / response to light stimulus / MAP kinase kinase activity / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm ...JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / response to light stimulus / MAP kinase kinase activity / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm / rhythmic process / cellular senescence / Oxidative Stress Induced Senescence / protein phosphorylation / protein serine kinase activity / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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 ...Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-FMY / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHabel, J.E. / Laughlin, J.D. / LoGrasso, P.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Synthesis, Biological Evaluation, X-ray Structure, and Pharmacokinetics of Aminopyrimidine c-jun-N-terminal Kinase (JNK) Inhibitors
Authors: Kamenecka, T. / Jiang, R. / Song, X. / Duckett, D. / Chen, W. / Ling, Y.Y. / Habel, J. / Laughlin, J.D. / Chambers, J. / Figuera-Losada, M. / Cameron, M.D. / Lin, L. / Ruiz, C.H. / Lograsso, P.V.
History
DepositionNov 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_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: Mitogen-activated protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6942
Polymers42,1921
Non-polymers5031
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.362, 125.642, 68.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Mitogen-activated protein kinase 10 / Stress-activated protein kinase JNK3 / c-Jun N-terminal kinase 3 / MAP kinase p49 3F12


Mass: 42191.832 Da / Num. of mol.: 1 / Fragment: residues 39-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK10, JNK3, JNK3A, PRKM10 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P53779, mitogen-activated protein kinase
#2: Chemical ChemComp-FMY / N-[(2Z)-4-(3-fluoro-5-morpholin-4-ylphenyl)pyrimidin-2(1H)-ylidene]-4-(3-morpholin-4-yl-1H-1,2,4-triazol-1-yl)aniline


Mass: 502.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27FN8O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.5
Details: 10MG/ML JNK3 MIXED WITH 1MM AMP-PCP, 2MM MGCL2, 0.4MM ZWITTERGENT 3-14, AND 10% ETHYLENE GLYCOL. CRYSTALS GROWN IN 0.2M NACL, 0.1M BIS-TRIS, 28-31% PEG 3350, PH 5.5. Ligand soaked in to ...Details: 10MG/ML JNK3 MIXED WITH 1MM AMP-PCP, 2MM MGCL2, 0.4MM ZWITTERGENT 3-14, AND 10% ETHYLENE GLYCOL. CRYSTALS GROWN IN 0.2M NACL, 0.1M BIS-TRIS, 28-31% PEG 3350, PH 5.5. Ligand soaked in to crystals., microbatch, temperature 293.0K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→68.29 Å / Num. obs: 13329 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.062

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FI3
Resolution: 2.4→23.38 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / SU B: 20.828 / SU ML: 0.228 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.507 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26933 708 5 %RANDOM
Rwork0.21957 ---
obs0.22205 13142 98.6 %-
all-13329 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.973 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å20 Å20 Å2
2--1.02 Å20 Å2
3---1.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.291 Å0.507 Å
Refinement stepCycle: LAST / Resolution: 2.4→23.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 37 27 2595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222636
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1071.9843587
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8845329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78323.925107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68215407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3421513
X-RAY DIFFRACTIONr_chiral_restr0.1270.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.0211982
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.211.51652
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13422638
X-RAY DIFFRACTIONr_scbond_it3.3473984
X-RAY DIFFRACTIONr_scangle_it4.7884.5948
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.395→2.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 57 -
Rwork0.322 858 -
obs--87.48 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
19.4226-3.27934.64913.9417-0.15239.72660.1042-0.25541.051-0.0032-0.2907-0.1663-0.4255-0.10570.18650.249-0.0020.0970.1986-0.07660.2986-28.40852.17815.855
23.5005-2.4876-1.440313.40663.84987.25240.0642-0.0630.16810.125-0.6231.08530.7641-0.690.55880.282-0.0810.08960.2883-0.10350.4151-35.08444.00213.159
311.2934-1.6297-4.29121.74940.18622.9999-0.5464-0.6957-0.25570.06240.1949-0.40650.59230.55960.35150.34980.05010.02310.3823-0.02210.3904-15.67543.27510.631
411.10477.05957.4075.30714.852118.16950.30430.3674-0.1835-0.13510.00290.13521.0122-0.4106-0.30720.47640.01730.03260.3031-0.07660.4753-17.99939.194-0.481
55.8427-8.48743.233912.7626-4.6151.81860.51980.2693-0.2185-1.2971-0.46220.58150.22720.1352-0.05760.85130.0637-0.19570.3335-0.0830.3403-29.83134.648-1.438
612.29585.4424-0.04748.28451.11243.8230.1607-0.05810.5624-0.06460.0947-0.1652-0.23170.1126-0.25530.25170.03250.03140.1989-0.0410.2753-22.08750.4918.231
73.44180.56911.714411.32710.64053.5285-0.1092-0.24170.09931.31730.18460.55670.1741-0.0259-0.07540.31020.01030.11580.3015-0.01380.2479-34.97119.92911.458
86.4447-0.5201-1.19364.55791.36563.2109-0.00940.04440.4497-0.01730.19190.0052-0.2350.1947-0.18250.2811-0.0334-0.03390.2257-0.03470.2885-26.40225.0341.43
92.2478-3.0356-0.96834.68371.45183.4382-0.1966-0.4080.33730.42570.5262-0.46360.12470.703-0.32960.32440.021-0.09140.4269-0.10380.2314-18.94820.5376.743
1012.5471-0.3859-2.84556.61290.50251.4982-0.6612-0.8902-0.33050.84770.6089-0.96030.41140.63210.05230.44290.2589-0.32280.7181-0.04440.3982-8.95410.92711.083
112.81444.75451.48198.4790.444213.25130.94690.0655-1.09871.8148-0.3458-1.70970.76573.2643-0.60111.02380.4759-0.38941.44640.22650.956-4.5976.35610.878
125.85261.10233.25477.67782.59173.5858-0.2808-0.6762-0.84991.51750.2371.36311.29090.32440.04381.26180.62470.51810.61370.38850.7241-30.0424.5556.133
137.6923-1.4973-0.55814.2102-0.20432.5757-0.18680.3547-0.2562-0.20760.12440.17730.18450.36950.06240.2883-0.0045-0.0610.2038-0.04640.1887-27.16613.206-4.773
1417.0178-1.9992-4.09175.1278-0.37164.2507-0.43821.04520.073-0.23130.2949-0.1966-0.3622-0.05530.14330.306-0.05610.07840.3105-0.01950.3615-11.22648.9140.835
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 64
2X-RAY DIFFRACTION2A65 - 89
3X-RAY DIFFRACTION3A90 - 105
4X-RAY DIFFRACTION4A106 - 118
5X-RAY DIFFRACTION5A119 - 127
6X-RAY DIFFRACTION6A128 - 148
7X-RAY DIFFRACTION7A149 - 166
8X-RAY DIFFRACTION8A167 - 200
9X-RAY DIFFRACTION9A201 - 261
10X-RAY DIFFRACTION10A262 - 291
11X-RAY DIFFRACTION11A292 - 309
12X-RAY DIFFRACTION12A310 - 343
13X-RAY DIFFRACTION13A344 - 363
14X-RAY DIFFRACTION14A383 - 401

+
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