[English] 日本語
Yorodumi
- PDB-9h47: EGFR wild type in complex with 26313 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9h47
TitleEGFR wild type in complex with 26313
ComponentsEpidermal growth factor receptor
KeywordsTRANSFERASE / KINASE / EGFR / INHIBITOR
Function / homology
Function and homology information


multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / response to UV-A ...multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / response to UV-A / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / Signaling by EGFR / ERBB2 Activates PTK6 Signaling / digestive tract morphogenesis / intracellular vesicle / eyelid development in camera-type eye / negative regulation of epidermal growth factor receptor signaling pathway / cerebral cortex cell migration / protein insertion into membrane / ERBB2 Regulates Cell Motility / protein tyrosine kinase activator activity / Respiratory syncytial virus (RSV) attachment and entry / Signaling by ERBB4 / PI3K events in ERBB2 signaling / positive regulation of phosphorylation / positive regulation of peptidyl-serine phosphorylation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hair follicle development / MAP kinase kinase kinase activity / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / embryonic placenta development / salivary gland morphogenesis / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in EGFR signaling / transmembrane receptor protein tyrosine kinase activity / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / ossification / basal plasma membrane / cellular response to epidermal growth factor stimulus / positive regulation of DNA repair / positive regulation of DNA replication / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Signal transduction by L1 / positive regulation of protein localization to plasma membrane / cellular response to amino acid stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / NOTCH3 Activation and Transmission of Signal to the Nucleus / cellular response to estradiol stimulus / clathrin-coated endocytic vesicle membrane / EGFR downregulation / Signaling by ERBB2 TMD/JMD mutants / cell-cell adhesion / Constitutive Signaling by EGFRvIII / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / negative regulation of protein catabolic process / positive regulation of miRNA transcription / epidermal growth factor receptor signaling pathway / kinase binding / ruffle membrane / Downregulation of ERBB2 signaling / positive regulation of fibroblast proliferation / cell morphogenesis / neuron differentiation / positive regulation of protein phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / HCMV Early Events / actin filament binding / cell junction / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / PIP3 activates AKT signaling / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / virus receptor activity / RAF/MAP kinase cascade / positive regulation of cell growth / protein tyrosine kinase activity / double-stranded DNA binding / early endosome membrane / protein phosphatase binding / nuclear membrane / basolateral plasma membrane / learning or memory / cell surface receptor signaling pathway / Extra-nuclear estrogen signaling / positive regulation of ERK1 and ERK2 cascade
Similarity search - Function
: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / : / 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
: / Epidermal growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.991 Å
AuthorsPintar, S. / Martin, M.P. / Noble, M.E.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKDRCDDRPGMApr2020100002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/X004872/1 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2026
Title: Covalent Alkynylpyridopyrimidinones Targeting Cysteine 775 of the Epidermal Growth Factor Receptor Overcome Resistance to Current Therapies.
Authors: Stewart, H.L. / Bordoni, C. / Jennings, C.E. / Al-Khawaldeh, I. / Martin, M.P. / Noble, R.A. / Phillips, N. / Pintar, S. / Prendergast, L. / Thomas, H.D. / Wang, L.Z. / Watt, J.E. / Wittner, ...Authors: Stewart, H.L. / Bordoni, C. / Jennings, C.E. / Al-Khawaldeh, I. / Martin, M.P. / Noble, R.A. / Phillips, N. / Pintar, S. / Prendergast, L. / Thomas, H.D. / Wang, L.Z. / Watt, J.E. / Wittner, A. / Bronowska, A.K. / Cano, C. / Noble, M.E.M. / Wedge, S.R. / Waring, M.J.
History
DepositionOct 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8502
Polymers37,4351
Non-polymers4151
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.59, 145.59, 145.59
Angle α, β, γ (deg.)90, 90, 90
Int Tables number197
Space group name H-MI23

-
Components

#1: Protein Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1


Mass: 37435.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB, ERBB1, HER1 / Production host: Escherichia coli (E. coli)
References: UniProt: P00533, receptor protein-tyrosine kinase
#2: Chemical ChemComp-A1IR9 / 2-[[4-[2-(dimethylamino)ethyl-methyl-amino]phenyl]amino]-8-phenyl-pyrido[2,3-d]pyrimidin-7-one


Mass: 414.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26N6O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.19 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 25 mM HEPES pH 8, 150 mM NaCl, 10 % glycerol, 1 mM DTT 85mM Tris pH 7.6, 140 mM acetate, 23.5 % Polyethylene glycol 4,000, 18% glycerol
PH range: 7.5-8.5

-
Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.99→46.04 Å / Num. obs: 10543 / % possible obs: 100 % / Redundancy: 40.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.451 / Net I/σ(I): 9.4
Reflection shellResolution: 2.99→3.17 Å / Redundancy: 41.2 % / Rmerge(I) obs: 6.905 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1673 / CC1/2: 0.38 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.991→46.04 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 20.341 / SU ML: 0.337 / Cross valid method: FREE R-VALUE / ESU R Free: 0.379
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2438 500 4.742 %
Rwork0.2002 10043 -
all0.202 --
obs-10543 99.962 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.991→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 31 0 2632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122693
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162595
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.8383647
X-RAY DIFFRACTIONr_angle_other_deg0.6021.7675997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3265324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg269.09122
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg18.925202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.11910489
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.09510116
X-RAY DIFFRACTIONr_chiral_restr0.0790.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023103
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02579
X-RAY DIFFRACTIONr_nbd_refined0.2580.2590
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.22454
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21312
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21432
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined1.0660.229
X-RAY DIFFRACTIONr_nbd_other0.420.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0210.22
X-RAY DIFFRACTIONr_mcbond_it10.86210.0671299
X-RAY DIFFRACTIONr_mcbond_other10.81810.071299
X-RAY DIFFRACTIONr_mcangle_it16.44118.0981622
X-RAY DIFFRACTIONr_mcangle_other16.44118.1031623
X-RAY DIFFRACTIONr_scbond_it11.22510.7131394
X-RAY DIFFRACTIONr_scbond_other11.22110.7141395
X-RAY DIFFRACTIONr_scangle_it17.27519.3592025
X-RAY DIFFRACTIONr_scangle_other17.27119.362026
X-RAY DIFFRACTIONr_lrange_it24.379122.86410857
X-RAY DIFFRACTIONr_lrange_other24.378122.86210858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.991-3.0680.456370.435722X-RAY DIFFRACTION100
3.068-3.1520.417360.366726X-RAY DIFFRACTION100
3.152-3.2430.33490.308674X-RAY DIFFRACTION100
3.243-3.3420.28300.283675X-RAY DIFFRACTION100
3.342-3.4510.319420.256645X-RAY DIFFRACTION100
3.451-3.5710.25280.238634X-RAY DIFFRACTION100
3.571-3.7050.213290.214624X-RAY DIFFRACTION100
3.705-3.8550.21440.209565X-RAY DIFFRACTION100
3.855-4.0260.216360.19560X-RAY DIFFRACTION100
4.026-4.220.271290.172545X-RAY DIFFRACTION100
4.22-4.4470.219180.156515X-RAY DIFFRACTION100
4.447-4.7140.251180.155503X-RAY DIFFRACTION100
4.714-5.0350.158160.151476X-RAY DIFFRACTION100
5.035-5.4330.17140.178432X-RAY DIFFRACTION100
5.433-5.9440.225260.189391X-RAY DIFFRACTION100
5.944-6.6320.346150.21380X-RAY DIFFRACTION100
6.632-7.6310.298170.183311X-RAY DIFFRACTION100
7.631-9.2830.21260.148293X-RAY DIFFRACTION100
9.283-12.8690.09340.163228X-RAY DIFFRACTION100
12.869-46.040.20860.31144X-RAY DIFFRACTION100

+
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