Macromolecule Content

Total Structure Weight: 73.44 kDa
Atom Count: 4,574
Modelled Residue Count: 557
Deposited Residue Count: 628
Unique protein chains: 1

3DTW

Crystal structure of the VEGFR2 kinase domain in complex with a benzisoxazole inhibitor

PDB DOI: https://doi.org/10.2210/pdb3DTW/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2008-07-16 Released: 2008-09-09
Deposition Author(s): Whittington, D.A., Long, A.M., Rose, P., Gu, Y., Zhao, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.279
R-Value Work: 0.215

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Discovery of amido-benzisoxazoles as potent c-Kit inhibitors.

Kunz, R.K., Rumfelt, S., Chen, N., Zhang, D., Tasker, A.S., Burli, R., Hungate, R., Yu, V., Nguyen, Y., Whittington, D.A., Meagher, K.L., Plant, M., Tudor, Y., Schrag, M., Xu, Y., Ng, G.Y., Hu, E.

(2008) Bioorg Med Chem Lett 18: 5115-5117

PubMed: 18723346 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.07.111
Primary Citation of Related Structures:
3DTW

PubMed Abstract:

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor receptor 2	A, B	314	Homo sapiens	Mutation(s): 3 Gene Names: KDR, FLK1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P35968 (Homo sapiens) Explore P35968 Go to UniProtKB: P35968
PHAROS: P35968
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35968
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A96 Query on A96 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	6-chloro-N-pyrimidin-5-yl-3-{[3-(trifluoromethyl)phenyl]amino}-1,2-benzisoxazole-7-carboxamide C₁₉ H₁₁ Cl F₃ N₅ O₂ FEGRQUWSKADGSP-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A, B	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
A96	BindingDB: 3DTW	IC50: 353 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.279
R-Value Work: 0.215
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.244	α = 90
b = 68.355	β = 92.16
c = 88.485	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-09-09

Deposition Author(s):

Whittington, D.A.

Revision History (Full details and data files)

Version 1.0: 2008-09-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-08-23
Changes: Source and taxonomy
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.