3HNG

Crystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide

• PDB DOI: https://doi.org/10.2210/pdb3HNG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-31 Released: 2009-06-30 
• Deposition Author(s): Tresaugues, L., Roos, A., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nyman, T., Persson, C., Kragh-Nielsen, T., Kotzch, A., Sagemark, J., Schueler, H., Schutz, P., Siponen, M.I., Svensson, L., Thorsell, A.G., Van der Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.260 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide

Tresaugues, L., Roos, A., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nyman, T., Persson, C., Kragh-Nielsen, T., Kotzch, A., Sagemark, J., Schueler, H., Schutz, P., Siponen, M.I., Svensson, L., Thorsell, A.G., Van der Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.45 kDa 
• Atom Count: 2,357 
• Modelled Residue Count: 288 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor receptor 1	A	360	Homo sapiens	Mutation(s): 0  Gene Names: FLT1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P17948 (Homo sapiens) Explore P17948  Go to UniProtKB:  P17948
PHAROS:  P17948 GTEx:  ENSG00000102755

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8ST	B [auth A]	N-(4-chlorophenyl)-2-[(pyridin-4-ylmethyl)amino]benzamide C19 H16 Cl N3 O GGPZCOONYBPZEW-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
8ST	BindingDB:  3HNG	IC50: 180 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.260 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.04	α = 90
b = 71.15	β = 90
c = 196.02	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Tresaugues, L., Roos, A., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nyman, T., Persson, C., Kragh-Nielsen, T., Kotzch, A., Sagemark, J., Schueler, H., Schutz, P., Siponen, M.I., Svensson, L., Thorsell, A.G., Van der Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description