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- PDB-3hng: Crystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-... -

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Entry
Database: PDB / ID: 3hng
TitleCrystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide
ComponentsVascular endothelial growth factor receptor 1VEGF receptor
KeywordsTRANSFERASE / RECEPTOR TYROSINE KINASE / VEGFR1 / FLT1 / KINASE DOMAIN / INHIBITOR / ACTIVATION LOOP / VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / SGC STOCKHOLM / Angiogenesis / ATP-binding / Cell membrane / Developmental protein / Differentiation / Disulfide bond / Glycoprotein / Immunoglobulin domain / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Secreted / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity / embryonic morphogenesis / negative regulation of vascular endothelial cell proliferation / blood vessel morphogenesis / growth factor binding ...vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity / embryonic morphogenesis / negative regulation of vascular endothelial cell proliferation / blood vessel morphogenesis / growth factor binding / monocyte chemotaxis / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / positive regulation of phospholipase C activity / transmembrane receptor protein tyrosine kinase activity / positive regulation of MAP kinase activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of angiogenesis / cell migration / actin cytoskeleton / angiogenesis / positive regulation of MAPK cascade / protein autophosphorylation / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / endosome / positive regulation of cell migration / focal adhesion / positive regulation of cell population proliferation / extracellular space / ATP binding / plasma membrane
Similarity search - Function
Vascular endothelial growth factor receptor 1 (VEGFR1) / VEGFR-2, transmembrane domain / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set ...Vascular endothelial growth factor receptor 1 (VEGFR1) / VEGFR-2, transmembrane domain / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-8ST / Vascular endothelial growth factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTresaugues, L. / Roos, A. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, 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)
CitationJournal: To be Published
Title: Crystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide
Authors: 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. / ...Authors: 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.
History
DepositionMay 31, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vascular endothelial growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4543
Polymers41,0811
Non-polymers3732
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.040, 71.150, 196.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Vascular endothelial growth factor receptor 1 / VEGF receptor / VEGFR-1 / Vascular permeability factor receptor / Tyrosine-protein kinase receptor FLT / Flt-1 / ...VEGFR-1 / Vascular permeability factor receptor / Tyrosine-protein kinase receptor FLT / Flt-1 / Tyrosine-protein kinase FRT / Fms-like tyrosine kinase 1


Mass: 41081.125 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP residues 801-1158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLT1 / Plasmid: pNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pRARE
References: UniProt: P17948, receptor protein-tyrosine kinase
#2: Chemical ChemComp-8ST / N-(4-chlorophenyl)-2-[(pyridin-4-ylmethyl)amino]benzamide


Mass: 337.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16ClN3O
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M potassium formate, 20% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2009 / Details: TOROIDAL ZERODUR MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→44.99 Å / Num. all: 11982 / Num. obs: 11958 / % possible obs: 99.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 65.8 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.078 / Net I/σ(I): 13.2
Reflection shellResolution: 2.67→2.81 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1669 / Rsym value: 0.441 / % possible all: 98.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
REFMAC5.5.0066refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QU5

2qu5


Resolution: 2.7→44.99 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.891 / SU B: 23.981 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.654 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26018 551 4.8 %RANDOM
Rwork0.19431 ---
all0.19739 11021 --
obs0.19739 10998 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.129 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--1.14 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 25 33 2348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222374
X-RAY DIFFRACTIONr_bond_other_d0.0010.022186
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9883196
X-RAY DIFFRACTIONr_angle_other_deg0.6435086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0775286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97623.168101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.82515433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5081518
X-RAY DIFFRACTIONr_chiral_restr0.0730.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212583
X-RAY DIFFRACTIONr_gen_planes_other00.021495
X-RAY DIFFRACTIONr_mcbond_it0.5471.51434
X-RAY DIFFRACTIONr_mcbond_other0.0941.5584
X-RAY DIFFRACTIONr_mcangle_it1.08622304
X-RAY DIFFRACTIONr_scbond_it1.5843940
X-RAY DIFFRACTIONr_scangle_it2.7274.5891
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 33 -
Rwork0.335 798 -
obs-798 97.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.84345.1424-6.79945.9662-5.80468.29981.5017-0.13790.64331.5686-0.4986-0.7771-2.08990.6879-1.00310.9245-0.3877-0.08291.00440.19771.360212.25533.56134.956
23.1897-0.42020.70731.35920.27634.94520.1324-0.2282-0.00830.0456-0.10850.04120.2883-0.0291-0.02390.0397-0.00470.01040.0860.02770.05823.70416.48637.955
33.95220.28270.67573.7270.33885.74720.00150.57070.052-0.32070.0732-0.19650.22580.7144-0.07470.13640.0289-0.00570.1750.00010.01675.60217.93515.633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A803 - 818
2X-RAY DIFFRACTION2A819 - 925
3X-RAY DIFFRACTION3A992 - 1158

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