3BE2	Transferase	date	Nov 16, 2007
title	Crystal Structure Of The Vegfr2 Kinase Domain In Complex Wit Benzamide Inhibitor
authors	D.A.Whittington, J.L.Kim, A.M.Long, Y.Gu, P.Rose, H.Zhao
compound		source
Molecule: Vascular Endothelial Growth Factor Receptor 2 Chain: A Fragment: Kinase Domain, Residues 815-939 And 990-1171 Synonym: Vegfr-2, Kinase Insert Domain Receptor, Protein-Ty Kinase Receptor Flk-1, Cd309 Antigen; Ec: 2.7.10.1 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Kdr, Flk1 Expression_system: Trichoplusia Ni Expression_system_common: Cabbage Looper Expression_system_taxid: 7111 Expression_system_vector_type: Baculovirus
symmetry	Space Group: P 1 21 1	R_factor 0.197 R_Free 0.226
crystal cell	length a length b length c angle alpha angle beta angle gamma 41.770 84.380 47.570 90.00 100.09 90.00
method	X-Ray Diffraction	resolution	1.75 Å
ligand	RAJ BindingDB	enzyme	Transferase E.C.2.7.10.1 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Naphthamides as novel and potent vascular endothelial growth factor receptor tyrosine kinase inhibitors: design, synthesis, and evaluation., Harmange JC, Weiss MM, Germain J, Polverino AJ, Borg G, Bready J, Chen D, Choquette D, Coxon A, Demelfi T, Dipietro L, Doerr N, Estrada J, Flynn J, Graceffa RF, Harriman SP, Kaufman S, La DS, Long A, Martin MW, Neervannan S, Patel VF, Potashman M, Regal K, Roveto PM, Schrag ML, Starnes C, Tasker A, Teffera Y, Wang L, White RD, Whittington DA, Zanon R, J Med Chem. 2008 Mar 27;51(6):1649-67. Epub 2008 Mar 7. PMID:18324761

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk] Biological Unit Coordinates (3be2.pdb1.gz) 53 Kb LPC: Ligand-Protein Contacts for 3BE2 CSU: Contacts of Structural Units for 3BE2 Likely Quarternary Molecular Structure file(s) for 3BE2 Structure Factors (283 Kb) Retrieve 3BE2 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3BE2 from S2C, [Save to disk] Re-refined 3be2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3BE2 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 3BE2

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 3D motif for 3BE2, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1b3be2, region E:4-178 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3be2_A] [3be2] SWISS-PROT database: [P35968] Domain organization of [VGFR2_HUMAN] by SWISSPFAM Domain found in 3BE2: [TyrKc ] by SMART

Other resources with information on 3BE2

Community annotation for 3BE2 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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