[English] 日本語
Yorodumi
- PDB-4l7f: Co-crystal Structure of JNK1 and AX13587 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l7f
TitleCo-crystal Structure of JNK1 and AX13587
ComponentsMitogen-activated protein kinase 8
KeywordsTransferase/Transferase Inhibitor / protein kinase fold / protein kinase / jun-c / phosphorylation / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


positive regulation of cell killing / JUN phosphorylation / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / JUN kinase activity / WNT5:FZD7-mediated leishmania damping / positive regulation of cyclase activity / histone deacetylase regulator activity ...positive regulation of cell killing / JUN phosphorylation / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / JUN kinase activity / WNT5:FZD7-mediated leishmania damping / positive regulation of cyclase activity / histone deacetylase regulator activity / positive regulation of NLRP3 inflammasome complex assembly / DSCAM interactions / NRAGE signals death through JNK / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / mitogen-activated protein kinase / regulation of macroautophagy / response to mechanical stimulus / response to UV / protein serine/threonine kinase binding / stress-activated MAPK cascade / JNK cascade / cellular response to cadmium ion / positive regulation of protein metabolic process / cellular response to amino acid starvation / NRIF signals cell death from the nucleus / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / negative regulation of protein binding / FCERI mediated MAPK activation / peptidyl-threonine phosphorylation / regulation of circadian rhythm / histone deacetylase binding / cellular response to reactive oxygen species / cellular response to mechanical stimulus / regulation of protein localization / cellular senescence / Signaling by ALK fusions and activated point mutants / rhythmic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to oxidative stress / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein phosphatase binding / Oxidative Stress Induced Senescence / response to oxidative stress / positive regulation of apoptotic process / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / synapse / positive regulation of gene expression / negative regulation of apoptotic process / enzyme binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
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-1V5 / Mitogen-activated protein kinase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWalter, R.L. / Ranieri, G.M. / Riggs, A.M. / Weissig, H. / Li, B. / Shreder, K.R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Hit-to-lead optimization and kinase selectivity of imidazo[1,2-a]quinoxalin-4-amine derived JNK1 inhibitors.
Authors: Li, B. / Cociorva, O.M. / Nomanbhoy, T. / Weissig, H. / Li, Q. / Nakamura, K. / Liyanage, M. / Zhang, M.C. / Shih, A.Y. / Aban, A. / Hu, Y. / Cajica, J. / Pham, L. / Kozarich, J.W. / Shreder, K.R.
History
DepositionJun 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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: Mitogen-activated protein kinase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8372
Polymers42,3771
Non-polymers4601
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.802, 135.802, 94.208
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Mitogen-activated protein kinase 8 / MAP kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated ...MAP kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated protein kinase JNK1 / c-Jun N-terminal kinase 1


Mass: 42377.102 Da / Num. of mol.: 1 / Fragment: UNP residues 7-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C
References: UniProt: P45983, mitogen-activated protein kinase
#2: Chemical ChemComp-1V5 / N-[1-(4-fluorophenyl)cyclopropyl]-4-[(trans-4-hydroxycyclohexyl)amino]imidazo[1,2-a]quinoxaline-8-carboxamide


Mass: 459.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26FN5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 3.95 Å3/Da / Density % sol: 68.82 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM
DetectorDate: Feb 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 47064

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 2.581 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1977 2380 5.1 %RANDOM
Rwork0.1605 ---
obs0.1624 47049 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.65 Å2 / Biso mean: 27.3579 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.28 Å20 Å2
2--0.55 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 34 449 3354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223211
X-RAY DIFFRACTIONr_bond_other_d0.0030.0226
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9884399
X-RAY DIFFRACTIONr_angle_other_deg3.612359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7745423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23424.43149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15215624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0281520
X-RAY DIFFRACTIONr_chiral_restr0.110.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022434
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0212
X-RAY DIFFRACTIONr_nbd_refined0.2080.21463
X-RAY DIFFRACTIONr_nbd_other0.2740.237
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22195
X-RAY DIFFRACTIONr_nbtor_other0.1270.25
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2357
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.230
X-RAY DIFFRACTIONr_mcbond_it1.0681.51965
X-RAY DIFFRACTIONr_mcangle_it1.7123116
X-RAY DIFFRACTIONr_scbond_it2.42831475
X-RAY DIFFRACTIONr_scangle_it3.8654.51245
LS refinement shellResolution: 1.95→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 172 -
Rwork0.222 3291 -
all-3463 -
obs--98.63 %

+
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://pdbjlvh1.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