3RCD Transferase Transferase Inhibitor date Mar 30, 2011
title Her2 Kinase Domain Complexed With Tak-285
authors K.Aertgeerts, R.Skene, S.Sogabe
compound source
Molecule: Receptor Tyrosine-Protein Kinase Erbb-2
Chain: A, B, C, D
Fragment: Unp Residues 713-1028
Synonym: Metastatic Lymph Node Gene 19 Protein, Mln 19, Pro Oncogene Neu, Proto-Oncogene C-Erbb-2, Tyrosine Kinase-Type Surface Receptor Her2, P185erbb2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Erbb2, Her2, Mln19, Neu, Ngl
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 1
R_factor 0.224 R_Free 0.294
length a length b length c angle alpha angle beta angle gamma
50.542 64.936 92.360 90.42 89.72 90.35
method X-Ray Diffractionresolution 3.21 Å
ligand 03P BindingDB enzyme Transferase E.C. BRENDA
A, D, C, B

Primary referenceDesign and Synthesis of Novel Human Epidermal Growth Factor Receptor 2 (HER2)/Epidermal Growth Factor Receptor (EGFR) Dual Inhibitors Bearing a Pyrrolo[3,2-d]pyrimidine Scaffold., Ishikawa T, Seto M, Banno H, Kawakita Y, Oorui M, Taniguchi T, Ohta Y, Tamura T, Nakayama A, Miki H, Kamiguchi H, Tanaka T, Habuka N, Sogabe S, Yano J, Aertgeerts K, Kamiyama K, J Med Chem. 2011 Nov 4. PMID:22003817
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (383 Kb) [Save to disk]
  • Biological Unit Coordinates (3rcd.pdb1.gz) 98 Kb
  • Biological Unit Coordinates (3rcd.pdb2.gz) 94 Kb
  • Biological Unit Coordinates (3rcd.pdb3.gz) 98 Kb
  • Biological Unit Coordinates (3rcd.pdb4.gz) 94 Kb
  • Biological Unit Coordinates (3rcd.pdb5.gz) 189 Kb
  • Biological Unit Coordinates (3rcd.pdb6.gz) 189 Kb
  • LPC: Ligand-Protein Contacts for 3RCD
  • CSU: Contacts of Structural Units for 3RCD
  • Structure Factors (113 Kb)
  • Retrieve 3RCD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RCD from S2C, [Save to disk]
  • Re-refined 3rcd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RCD in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3RCD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3RCD, from MSDmotif at EBI
  • Fold representative 3rcd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rcd_D] [3rcd_A] [3rcd] [3rcd_C] [3rcd_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3RCD: [TyrKc ] by SMART
  • Other resources with information on 3RCD
  • Community annotation for 3RCD at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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