[English] 日本語
Yorodumi
- PDB-2puu: Crystal structure of p38 complex with 1-(5-tert-Butyl-2-p-tolyl-2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2puu
TitleCrystal structure of p38 complex with 1-(5-tert-Butyl-2-p-tolyl-2H-pyrazol-3-yl)-3-[4-(6-morpholin-4-ylmethyl-pyridin-3-yl)naphthalen-1-yl]urea
ComponentsMitogen-activated protein kinase 14
KeywordsTRANSFERASE / p38alpha / MAP kinases / drug discovery
Function / homology
Function and homology information


p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / myoblast differentiation involved in skeletal muscle regeneration / Regulation of MITF-M-dependent genes involved in pigmentation / NLRP1 inflammasome complex assembly / cell surface receptor protein serine/threonine kinase signaling pathway / ADP signalling through P2Y purinoceptor 1 ...p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / myoblast differentiation involved in skeletal muscle regeneration / Regulation of MITF-M-dependent genes involved in pigmentation / NLRP1 inflammasome complex assembly / cell surface receptor protein serine/threonine kinase signaling pathway / ADP signalling through P2Y purinoceptor 1 / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Oxidative Stress Induced Senescence / Myogenesis / Regulation of TP53 Activity through Phosphorylation / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / response to muramyl dipeptide / VEGFA-VEGFR2 Pathway / regulation of ossification / chondrocyte differentiation / fatty acid oxidation / striated muscle cell differentiation / regulation of synaptic membrane adhesion / stress-induced premature senescence / positive regulation of myoblast fusion / cartilage condensation / stress-activated protein kinase signaling cascade / skeletal muscle tissue development / positive regulation of cyclase activity / positive regulation of myotube differentiation / response to dietary excess / cellular response to UV-B / mitogen-activated protein kinase p38 binding / NFAT protein binding / regulation of cytokine production involved in inflammatory response / cellular response to lipoteichoic acid / p38MAPK cascade / positive regulation of cardiac muscle cell proliferation / response to muscle stretch / MAP kinase activity / cellular response to vascular endothelial growth factor stimulus / mitogen-activated protein kinase / lipopolysaccharide-mediated signaling pathway / positive regulation of brown fat cell differentiation / vascular endothelial growth factor receptor signaling pathway / pyroptotic inflammatory response / stress-activated MAPK cascade / positive regulation of myoblast differentiation / negative regulation of hippo signaling / placenta development / osteoclast differentiation / positive regulation of interleukin-12 production / cell morphogenesis / DNA damage checkpoint signaling / signal transduction in response to DNA damage / Neutrophil degranulation / positive regulation of D-glucose import across plasma membrane / positive regulation of erythrocyte differentiation / tumor necrosis factor-mediated signaling pathway / glucose metabolic process / response to insulin / cellular response to ionizing radiation / cellular response to tumor necrosis factor / cellular response to virus / positive regulation of protein import into nucleus / negative regulation of canonical Wnt signaling pathway / protein maturation / bone development / peptidyl-serine phosphorylation / kinase activity / positive regulation of reactive oxygen species metabolic process / osteoblast differentiation / angiogenesis / MAPK cascade / protein autophosphorylation / cellular response to lipopolysaccharide / response to lipopolysaccharide / spindle pole / protein phosphatase binding / protein kinase activity / protein phosphorylation / nuclear speck / intracellular signal transduction / apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / regulation of transcription by RNA polymerase II / DNA damage response / regulation of DNA-templated transcription / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain ...Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Phosphorylase Kinase; domain 1 / 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-G2G / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsQian, K.C.
CitationJournal: To be Published
Title: A new class of p38 MAP kinase inhibitors based on the pyrazole-naphthyl urea scaffold
Authors: Qian, K.C.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitogen-activated protein kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3762
Polymers39,8011
Non-polymers5761
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.908, 74.722, 78.245
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Mitogen-activated protein kinase 14 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha / CRK1


Mass: 39800.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14, Crk1, Csbp1, Csbp2 / Production host: Escherichia coli (E. coli)
References: UniProt: P47811, mitogen-activated protein kinase
#2: Chemical ChemComp-G2G / 5-TERT-BUTYL-2-(4-METHYLPHENYL)-3-{[({4-[6-(MORPHOLIN-4-YLMETHYL)PYRIDIN-3-YL]-1-NAPHTHYL}AMINO)CARBONYL]AMINO}-1H-PYRAZOL-2-IUM


Mass: 575.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H39N6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 10-20 % PEG4000, pH 6.0-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 11577

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.318 597 4.3 %
Rwork0.228 --
obs-11577 83.3 %
Displacement parametersBiso mean: 38.133 Å2
Baniso -1Baniso -2Baniso -3
1--2.118 Å20 Å20 Å2
2--9.092 Å20 Å2
3----6.974 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 43 31 2744
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4551.5
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_mcangle_it2.5162
X-RAY DIFFRACTIONc_scangle_it2.9032.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2birb1017.par
X-RAY DIFFRACTION3water_rep.param

+
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