Compound three letter code : YY3
 
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Entry Information
Entry status  (1)
REL
(10)
 
Experimental methods  (1)
X-ray diffraction
(10)
 
Authors  (44)
Ayaz P
(4)
Beyett TS
(4)
Choi HG
(4)
De Clercq DJH
(4)
Eck MJ
(4)
Gomez G
(4)
Gray NS
(4)
Heppner DE
(4)
Huang X
(4)
Jang J
(4)
Janne PA
(4)
Li JL
(4)
Liang L
(4)
Rana JK
(4)
Schmoker AM
(4)
Scott DA
(4)
Shan Y
(4)
Shaw DE
(4)
To C
(4)
Wu YC
(4)
Yan XE
(4)
Yun CH
(4)
Zhang CH
(4)
Zhao P
(4)
Zhu SJ
(4)
Chiba T
(1)
Dickson JM
(1)
Endo M
(1)
Flanagan JU
(1)
Fukami TA
(1)
Kashima K
(1)
Kawauchi H
(1)
McKeage M
(1)
McKeage MJ
(1)
Patterson AV
(1)
Sakamoto H
(1)
Sato S
(1)
Silva S
(1)
Smaill JB
(1)
Squire CJ
(1)
Tachibana Y
(1)
Tanimura H
(1)
Torizawa T
(1)
Yosaatmadja Y
(1)
 
Homo / hetero assembly  (1)
homo
(10)
 
Assembly composition  (1)
protein structure
(10)
 
Assembly polymer count  (2)
monomer
(6)
dimer
(4)
 
Resolution distribution
2.0 - 2.5
(5)
2.5 - 3
(5)
 
Release year distribution
2010 - 2015
(1)
2015 - 2020
(6)
2020 - 2025
(9)
 
Journal  (4)
J Med Chem
(4)
Nat Commun
(4)
J Struct Biol
(1)
Mol Cancer Ther
(1)
 
Macromolecules
Organism superkingdom  (1)
Eukaryota
(10)
 
Organism name  (1)
Homo sapiens
(10)
 
Molecule name  (3)
Epidermal growth factor receptor
(10)
Proto-oncogene c-ErbB-1
(10)
Receptor tyrosine-protein kinase erbB-1
(10)
 
Molecule type  (1)
Protein
(10)
 
Gene names  (4)
EGFR
(10)
ERBB
(10)
ERBB1
(10)
HER1
(10)
 
Interacting ligands  (7)
YY3 : N-(2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxy-5-{[4-(1-methyl-1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)prop-2-enamide
(10)
ANP : PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
(2)
CL : CHLORIDE ION
(2)
MG : MAGNESIUM ION
(2)
VNS : (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-{6-[4-(1-methylpiperidin-4-yl)phenyl]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}-N-(1,3-thiazol-2-yl)acetamide
(2)
9LL : (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)-N-(1,3-thiazol-2-yl)acetamide
(1)
JBJ : (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-{1-oxo-6-[4-(piperazin-1-yl)phenyl]-1,3-dihydro-2H-isoindol-2-yl}-N-(1,3-thiazol-2-yl)acetamide
(1)
 
Function and Biology
EC number / name  (1)
2.7.10.1 : Receptor protein-tyrosine kinase
(10)
 
Biological function  (3)
ATP binding
(10)
protein kinase activity
(10)
protein tyrosine kinase activity
(10)
 
Biological process  (1)
protein phosphorylation
(10)
 
Sequence and Structure classification
CATH class  (2)
Alpha Beta
(1)
Mainly Alpha
(1)
 
CATH topology  (2)
Phosphorylase Kinase; domain 1
(1)
Transferase(Phosphotransferase); domain 1
(1)
 
Pfam accession / name  (1)
PF07714 : PK_Tyr_Ser-Thr
(10)
 
Experimental Information
Diffraction protocol  (1)
Single wavelength
(10)
 
Diffraction radiation source type  (2)
Synchrotron
(9)
Rotating anode
(1)
 
Diffraction source  (7)
APS BEAMLINE 24-ID-E
(3)
APS BEAMLINE 19-ID
(2)
APS BEAMLINE 24-ID-C
(1)
PHOTON FACTORY BEAMLINE BL-17A
(1)
RIGAKU MICROMAX-007 HF
(1)
SSRF BEAMLINE BL18U1
(1)
SSRF BEAMLINE BL19U1
(1)
 
Synchrotron site  (3)
APS
(6)
SSRF
(2)
Photon Factory
(1)
 
Diffraction detector type  (3)
Pixel
(7)
CCD
(2)
Image plate
(1)
 
Refinement software  (2)
PHENIX
(9)
REFMAC
(1)
 
Representative Structures
Representative Structures
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Entries 1 to 10 of 10
Entries 1 to 10 of 10
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EGFR kinase (T790M/V948R) in complex with osimertinib and JBJ-04-125-02
Beyett TS, Eck MJ
Nat Commun (2022)
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: ANP    JBJ    MG    ANP    JBJ    MG    YY3    YY3   
Assembly name: Epidermal growth factor receptor (Preferred)   search this complex
PDBe complex ID: PDB-CPX-132701 (Preferred)   search this ID
PDBe-KB: P00533   
X-ray diffraction
2.16Å resolution
Released: 8 Sep 2021
Model geometry
Fit model/data
7jxp
7jxp
7jxp
EGFR kinase (T790M/V948R) in complex with osimertinib and EAI045
Beyett TS, Eck MJ
Nat Commun (2022)
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: ANP    MG    9LL    ANP    MG    YY3    9LL    YY3   
Assembly name: Epidermal growth factor receptor (Preferred)   search this complex
PDBe complex ID: PDB-CPX-132701 (Preferred)   search this ID
PDBe-KB: P00533   
X-ray diffraction
2.192Å resolution
Released: 8 Sep 2021
Model geometry
Fit model/data
7jxm
7jxm
7jxm
Crystal Structure of EGFR(L858R/T790M/C797S) in complex with Osimertinib
Kawauchi H, Fukami TA, Sato S, Endo M, Torizawa T, Kashima K, Chiba T, Sakamoto H
Mol Cancer Ther (2020) [PMID: 32943545  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: YY3    YY3   
Assembly name: Epidermal growth factor receptor (Preferred)   search this complex
PDBe complex ID: PDB-CPX-132671 (Preferred)   search this ID
PDBe-KB: P00533   
X-ray diffraction
2.05Å resolution
Released: 7 Oct 2020
Model geometry
Fit model/data
6lud
6lud
6lud
Crystal structure of EGFR 696-1022 WT in complex with AZD9291 prepared by cocrystallization
Yun CH, Zhu SJ, Yan XE
J Med Chem (2020) [PMID: 32672461  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: CL    YY3    YY3   
Assembly name: Epidermal growth factor receptor (Preferred)   search this complex
PDBe complex ID: PDB-CPX-132671 (Preferred)   search this ID
PDBe-KB: P00533   
X-ray diffraction
2.307Å resolution
Released: 29 Apr 2020
Model geometry
Fit model/data
6jxt
6jxt
6jxt
Crystal structure of EGFR 696-1022 T790M in complex with AZD9291 prepared by co-crystallization
Yun CH, Yan XE, Zhu SJ
J Med Chem (2020) [PMID: 32672461  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: CL    YY3    YY3   
Assembly name: Epidermal growth factor receptor (Preferred)   search this complex
PDBe complex ID: PDB-CPX-132671 (Preferred)   search this ID
PDBe-KB: P00533   
X-ray diffraction
2.53Å resolution
Released: 22 Apr 2020
Model geometry
Fit model/data
6jx0
6jx0
6jx0
Crystal structure of EGFR 696-1022 L858R in complex with AZD9291
Yun CH, Zhu SJ, Yan XE
J Med Chem (2020) [PMID: 32672461  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: YY3    YY3   
Assembly name: Epidermal growth factor receptor (Preferred)   search this complex
PDBe complex ID: PDB-CPX-132671 (Preferred)   search this ID
PDBe-KB: P00533   
X-ray diffraction
2.551Å resolution
Released: 22 Apr 2020
Model geometry
Fit model/data
6jwl
6jwl
6jwl
EGFR L858R/V948R in complex with osimertinib and allosteric inhibitor JBJ-09-063
Beyett TS, Eck MJ
Nat Commun (2022)
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: VNS    VNS    YY3    YY3   
Assembly name: Epidermal growth factor receptor (Preferred)   search this complex
PDBe complex ID: PDB-CPX-132701 (Preferred)   search this ID
PDBe-KB: P00533   
X-ray diffraction
2.602Å resolution
Released: 15 Sep 2021
Model geometry
Fit model/data
7k1h
7k1h
7k1h
AZD9291 complex with wild type EGFR
Squire CJ, Yosaatmadja Y, Flanagan JU, McKeage M
J Struct Biol (2015) [PMID: 26522274  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: YY3    YY3   
Assembly name: Epidermal growth factor receptor (Preferred)   search this complex
PDBe complex ID: PDB-CPX-132671 (Preferred)   search this ID
PDBe-KB: P00533   
X-ray diffraction
2.8Å resolution
Released: 11 Nov 2015
Model geometry
Fit model/data
4zau
4zau
4zau
EGFR kinase (T790M/V948R) in complex with osimertinib and JBJ-09-063
Beyett TS, Eck MJ
Nat Commun (2022)
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: VNS    VNS    YY3    YY3   
Assembly name: Epidermal growth factor receptor (Preferred)   search this complex
PDBe complex ID: PDB-CPX-132701 (Preferred)   search this ID
PDBe-KB: P00533   
X-ray diffraction
2.5Å resolution
Released: 8 Sep 2021
Model geometry
Fit model/data
7jxw
7jxw
7jxw
Crystal structure of EGFR 696-1022 T790M in complex with AZD9291 prepared by soaking
Zhu SJ, Yan XE, Yun CH
J Med Chem (2020) [PMID: 32672461  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: YY3    YY3   
Assembly name: Epidermal growth factor receptor (Preferred)   search this complex
PDBe complex ID: PDB-CPX-132671 (Preferred)   search this ID
PDBe-KB: P00533   
X-ray diffraction
2.531Å resolution
Released: 22 Apr 2020
Model geometry
Fit model/data
6jx4
6jx4
6jx4
Entries 1 to 10 of 10
Entries 1 to 10 of 10