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- PDB-3lvp: Crystal structure of bisphosphorylated IGF1-R Kinase domain (2P) ... -

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Basic information

Entry
Database: PDB / ID: 3lvp
TitleCrystal structure of bisphosphorylated IGF1-R Kinase domain (2P) in complex with a bis-azaindole inhibitor
ComponentsInsulin-like growth factor 1 receptor
KeywordsTRANSFERASE / protein kinase / tyrosine kinase / tyrosine phosphorylation / protein-substrate complex
Function / homology
Function and homology information


cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / protein kinase complex / protein transporter activity / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / negative regulation of muscle cell apoptotic process ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / protein kinase complex / protein transporter activity / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / cellular response to zinc ion starvation / cellular response to aldosterone / insulin receptor complex / negative regulation of hepatocyte apoptotic process / cellular response to testosterone stimulus / insulin-like growth factor I binding / insulin receptor activity / transcytosis / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / positive regulation of protein-containing complex disassembly / cellular response to angiotensin / cellular response to insulin-like growth factor stimulus / response to L-glutamate / dendritic spine maintenance / insulin binding / establishment of cell polarity / negative regulation of MAPK cascade / positive regulation of axon regeneration / amyloid-beta clearance / positive regulation of cytokinesis / positive regulation of osteoblast proliferation / regulation of JNK cascade / estrous cycle / insulin receptor substrate binding / G-protein alpha-subunit binding / response to vitamin E / SHC-related events triggered by IGF1R / phosphatidylinositol 3-kinase binding / peptidyl-tyrosine autophosphorylation / cellular response to transforming growth factor beta stimulus / T-tubule / cerebellum development / cellular response to dexamethasone stimulus / axonogenesis / insulin-like growth factor receptor signaling pathway / response to nicotine / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to estradiol stimulus / caveola / hippocampus development / cellular response to glucose stimulus / positive regulation of smooth muscle cell proliferation / insulin receptor binding / receptor protein-tyrosine kinase / cellular response to mechanical stimulus / cellular response to amyloid-beta / cellular senescence / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / protein tyrosine kinase activity / response to ethanol / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration / immune response / axon / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / protein-containing complex binding / negative regulation of apoptotic process / signal transduction / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats ...Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / 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 / 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-PDR / Insulin-like growth factor 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMaignan, S. / Marquette, J.P. / Guilloteau, J.P.
CitationJournal: Chem.Biol.Drug Des. / Year: 2010
Title: Design of Potent IGF1-R Inhibitors Related to Bis-azaindoles
Authors: Nemecek, C. / Metz, W.A. / Wentzler, S. / Ding, F.X. / Venot, C. / Souaille, C. / Dagallier, A. / Maignan, S. / Guilloteau, J.P. / Bernard, F. / Henry, A. / Grapinet, S. / Lesuisse, D.
History
DepositionFeb 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Insulin-like growth factor 1 receptor
B: Insulin-like growth factor 1 receptor
C: Insulin-like growth factor 1 receptor
D: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,67811
Polymers153,8774
Non-polymers1,8027
Water23413
1
A: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1464
Polymers38,4691
Non-polymers6773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9083
Polymers38,4691
Non-polymers4392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8122
Polymers38,4691
Non-polymers3431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8122
Polymers38,4691
Non-polymers3431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.950, 94.950, 322.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Insulin-like growth factor 1 receptor / / IGF1R / Insulin-like growth factor I receptor / IGF-I receptor / Insulin-like growth factor 1 ...IGF1R / Insulin-like growth factor I receptor / IGF-I receptor / Insulin-like growth factor 1 receptor alpha chain / Insulin-like growth factor 1 receptor beta chain


Mass: 38469.156 Da / Num. of mol.: 4 / Fragment: kinase domain (2P)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1R / Production host: Escherichia coli (E. coli)
References: UniProt: P08069, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-PDR / 3-(4-chloro-1H-pyrrolo[2,3-b]pyridin-2-yl)-5,6-dimethoxy-1-methyl-1H-pyrrolo[3,2-b]pyridine


Mass: 342.780 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H15ClN4O2
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.4M Ammonium Sulfate, 100mM Hepes, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 30251 / Num. obs: 29918 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 5.9

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K3A

1k3a


Resolution: 3→30 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection
Rfree0.279 1517
Rwork0.226 -
all0.226 -
obs-29554
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9274 0 118 13 9405

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