[English] 日本語
Yorodumi
- PDB-8jf3: C-Src in complex with compound 9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jf3
TitleC-Src in complex with compound 9
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE/Inhibitor / TRANSFERASE-Inhibitor complex
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway ...regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway / Regulation of gap junction activity / BMP receptor binding / negative regulation of focal adhesion assembly / positive regulation of integrin activation / Activated NTRK2 signals through FYN / positive regulation of protein processing / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / negative regulation of neutrophil activation / regulation of vascular permeability / focal adhesion assembly / connexin binding / Activated NTRK3 signals through PI3K / osteoclast development / cellular response to fluid shear stress / signal complex assembly / positive regulation of small GTPase mediated signal transduction / branching involved in mammary gland duct morphogenesis / Co-stimulation by CD28 / Regulation of RUNX1 Expression and Activity / DCC mediated attractive signaling / EPH-Ephrin signaling / positive regulation of podosome assembly / regulation of bone resorption / positive regulation of lamellipodium morphogenesis / Ephrin signaling / Signal regulatory protein family interactions / podosome / odontogenesis / negative regulation of mitochondrial depolarization / MET activates PTK2 signaling / cellular response to peptide hormone stimulus / Regulation of KIT signaling / regulation of early endosome to late endosome transport / leukocyte migration / Signaling by ALK / phospholipase activator activity / oogenesis / GP1b-IX-V activation signalling / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Receptor Mediated Mitophagy / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / stress fiber assembly / positive regulation of Notch signaling pathway / Signaling by EGFR / RUNX2 regulates osteoblast differentiation / stimulatory C-type lectin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of cell-cell adhesion / Recycling pathway of L1 / PECAM1 interactions / uterus development / regulation of heart rate by cardiac conduction / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / protein tyrosine kinase activator activity / RET signaling / negative regulation of anoikis / Long-term potentiation / signaling receptor activator activity / FCGR activation / positive regulation of epithelial cell migration / EPH-ephrin mediated repulsion of cells / positive regulation of protein serine/threonine kinase activity / GAB1 signalosome / negative regulation of hippo signaling / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / bone resorption / negative regulation of protein-containing complex assembly / forebrain development / Downregulation of ERBB4 signaling / progesterone receptor signaling pathway / Nuclear signaling by ERBB4 / InlA-mediated entry of Listeria monocytogenes into host cells / phospholipase binding / T cell costimulation / cellular response to platelet-derived growth factor stimulus / p38MAPK events / ephrin receptor binding / Signaling by ERBB2 / EPHB-mediated forward signaling / Integrin signaling / positive regulation of TORC1 signaling / NCAM signaling for neurite out-growth / ionotropic glutamate receptor binding
Similarity search - Function
: / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...: / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84647631109 Å
AuthorsZhang, Z.M. / Huang, H.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Global Reactivity Profiling of the Catalytic Lysine in Human Kinome for Covalent Inhibitor Development.
Authors: Tang, G. / Wang, W. / Zhu, C. / Huang, H. / Chen, P. / Wang, X. / Xu, M. / Sun, J. / Zhang, C.J. / Xiao, Q. / Gao, L. / Zhang, Z.M. / Yao, S.Q.
History
DepositionMay 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Src
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8684
Polymers64,7682
Non-polymers1,0992
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.716, 63.427, 73.649
Angle α, β, γ (deg.)101.214, 91.048, 90.161
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 32384.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1 / Production host: Escherichia coli (E. coli)
References: UniProt: P12931, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-C0N / 2-[4-[4-[bis(oxidanylidene)-$l^5-sulfanyl]oxyphenyl]carbonylpiperazin-1-yl]-6-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-N-prop-2-ynyl-pyrimidine-4-carboxamide


Mass: 549.582 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H25N8O5S
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 300 mM Sodium Acetate, 0.1 M MES pH 7.5, 4% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.84→72.23 Å / Num. obs: 16792 / % possible obs: 96.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 34.3720629344 Å2 / CC1/2: 0.991 / Net I/σ(I): 5.5
Reflection shellResolution: 2.84→2.94 Å / Num. unique obs: 16792 / CC1/2: 0.894

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84647631109→62.2147194464 Å / SU ML: 0.506517564523 / Cross valid method: FREE R-VALUE / σ(F): 1.97311662566 / Phase error: 35.3254243612
RfactorNum. reflection% reflection
Rfree0.316930785964 1685 10.0477042338 %
Rwork0.274171879585 15085 -
obs0.278454516745 16770 96.5791292329 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.2139186642 Å2
Refinement stepCycle: LAST / Resolution: 2.84647631109→62.2147194464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 78 0 3853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002707192095933949
X-RAY DIFFRACTIONf_angle_d0.6651841637585365
X-RAY DIFFRACTIONf_chiral_restr0.023116858326585
X-RAY DIFFRACTIONf_plane_restr0.00272214345272674
X-RAY DIFFRACTIONf_dihedral_angle_d14.99696651941441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8465-2.93020.3685344281941500.323628328151278X-RAY DIFFRACTION97.2089857046
2.9302-3.02480.3813210161831290.3158876952331267X-RAY DIFFRACTION97.6906927922
3.0248-3.13290.38701334921400.3145929112571263X-RAY DIFFRACTION97.3629424011
3.1329-3.25830.3506725142471420.3027414727291264X-RAY DIFFRACTION96.8319559229
3.2583-3.40660.3169446372041370.2728803077741257X-RAY DIFFRACTION96.9401947149
3.4066-3.58620.3370167570881410.2852152016071257X-RAY DIFFRACTION96.8814968815
3.5862-3.81090.338671375371480.276200742441278X-RAY DIFFRACTION96.2862930452
3.8109-4.10510.3020329359011410.2652101936111228X-RAY DIFFRACTION96.3406052076
4.1051-4.51810.3000479970571390.2455594891631267X-RAY DIFFRACTION96.169630643
4.5181-5.17160.2895401816851380.2467341570431242X-RAY DIFFRACTION96.1002785515
5.1716-6.51450.3068696644971420.2807359742681253X-RAY DIFFRACTION97.1448467967
6.5145-100.2579720212481380.2495165688211231X-RAY DIFFRACTION94.1540577717

+
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