3B8R	Transferase	date	Nov 01, 2007
title	Crystal Structure Of The Vegfr2 Kinase Domain In Complex Wit Naphthamide Inhibitor
authors	D.A.Whittington, A.M.Long, Y.Gu, H.Zhao
compound		source
Molecule: Vascular Endothelial Growth Factor Receptor 2 Chain: A, B Fragment: Kinase Domain; Unp Residues 815-939, 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 0.204 R_Free 0.259
crystal cell	length a length b length c angle alpha angle beta angle gamma 55.436 67.972 87.687 90.00 91.36 90.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	887, EDO BindingDB	enzyme	Transferase E.C.2.7.10.1 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Evaluation of a series of naphthamides as potent, orally active vascular endothelial growth factor receptor-2 tyrosine kinase inhibitors., Weiss MM, Harmange JC, Polverino AJ, Bauer D, Berry L, Berry V, Borg G, Bready J, Chen D, Choquette D, Coxon A, Demelfi T, Doerr N, Estrada J, Flynn J, Graceffa RF, Harriman SP, Kaufman S, La DS, Long A, Neervannan S, Patel VF, Potashman M, Regal K, Roveto PM, Schrag ML, Starnes C, Tasker A, Teffera Y, Whittington DA, Zanon R, J Med Chem. 2008 Mar 27;51(6):1668-80. Epub 2008 Mar 7. PMID:18324759

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (99 Kb) [Save to disk] Biological Unit Coordinates (3b8r.pdb1.gz) 51 Kb Biological Unit Coordinates (3b8r.pdb2.gz) 46 Kb LPC: Ligand-Protein Contacts for 3B8R CSU: Contacts of Structural Units for 3B8R Likely Quarternary Molecular Structure file(s) for 3B8R Structure Factors (158 Kb) Retrieve 3B8R in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3B8R from S2C, [Save to disk] Re-refined 3b8r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3B8R 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 3B8R

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 3B8R, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3b8r_B] [3b8r] [3b8r_A] SWISS-PROT database: [P35968] Domain organization of [VGFR2_HUMAN] by SWISSPFAM Domain found in 3B8R: [TyrKc ] by SMART

Other resources with information on 3B8R

Community annotation for 3B8R at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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