Macromolecule Content

Total Structure Weight: 73.31 kDa
Atom Count: 4623
Residue Count: 549
Unique protein chains: 1

3EFL

Crystal structure of the VEGFR2 kinase domain in complex with motesanib

DOI: 10.2210/pdb3EFL/pdb

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

Deposited: 2008-09-09 Released: 2009-09-15
Deposition Author(s): Kim, J.L., Whittington, D.A., Long, A.M., Rose, P., Gu, Y., Zhao, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.264
R-Value Work: 0.230

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Discovery of Motesanib

Tasker, A.S., Patel, V.F.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor receptor 2	A, B	314	Homo sapiens	Mutation(s): 2 Gene Names: KDR, FLK1 EC: 2.7.10.1
Find proteins for P35968 (Homo sapiens) Explore P35968 Go to UniProtKB: P35968
NIH Common Fund Data Resources
PHAROS: P35968 GTEx: ENSG00000128052
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
706 Query on 706 Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [B] MOL2 format, chain C [A] MOL2 format, chain D [B]	A, B	N-(3,3-dimethyl-2,3-dihydro-1H-indol-6-yl)-2-[(pyridin-4-ylmethyl)amino]pyridine-3-carboxamide C₂₂ H₂₃ N₅ O RAHBGWKEPAQNFF-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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
706	IC50: 3 nM BindingDB
706	Kd: 26 nM BindingDB
706	Ki: 3 nM BindingDB

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.264
R-Value Work: 0.230
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.59	α = 90
b = 66.81	β = 93.27
c = 91.42	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2008-09-09
Released Date: 2009-09-15

Deposition Author(s):

Whittington, D.A.

Revision History

Version 1.0: 2009-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-08-23
Changes: Source and taxonomy

RCSB PDB is 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.