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- PDB-8pyk: Human IGF1R with inhibitor 47 -

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Basic information

Entry
Database: PDB / ID: 8pyk
TitleHuman IGF1R with inhibitor 47
ComponentsInsulin-like growth factor 1 receptor beta chain
KeywordsTRANSFERASE / Tyrosine / Kinase
Function / homology
Function and homology information


cardiac atrium development / negative regulation of cholangiocyte apoptotic process / protein kinase complex / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / insulin-like growth factor binding / IRS-related events triggered by IGF1R / protein transporter activity / negative regulation of muscle cell apoptotic process ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / protein kinase complex / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / insulin-like growth factor binding / IRS-related events triggered by IGF1R / protein transporter activity / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / cellular response to aldosterone / cellular response to zinc ion starvation / insulin receptor complex / insulin-like growth factor I binding / cellular response to testosterone stimulus / insulin receptor activity / transcytosis / negative regulation of hepatocyte apoptotic process / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / cellular response to angiotensin / positive regulation of protein-containing complex disassembly / dendritic spine maintenance / insulin binding / response to L-glutamate / cellular response to insulin-like growth factor stimulus / establishment of cell polarity / positive regulation of cytokinesis / positive regulation of axon regeneration / positive regulation of osteoblast proliferation / amyloid-beta clearance / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / insulin receptor substrate binding / G-protein alpha-subunit binding / response to vitamin E / estrous cycle / negative regulation of MAPK cascade / SHC-related events triggered by IGF1R / phosphatidylinositol 3-kinase binding / peptidyl-tyrosine autophosphorylation / cellular response to transforming growth factor beta stimulus / T-tubule / phosphatidylinositol 3-kinase/protein kinase B signal transduction / axonogenesis / cellular response to dexamethasone stimulus / cerebellum development / insulin-like growth factor receptor signaling pathway / hippocampus development / cellular response to estradiol stimulus / response to nicotine / cellular response to glucose stimulus / positive regulation of smooth muscle cell proliferation / insulin receptor binding / receptor protein-tyrosine kinase / caveola / 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 / protein autophosphorylation / positive regulation of MAPK cascade / Extra-nuclear estrogen signaling / 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 / identical protein binding / membrane / 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 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Similarity search - Domain/homology
Chem-IC2 / NICKEL (II) ION / Insulin-like growth factor 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsDreyer, M.K. / Wang, J. / Elkins, J.M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines InitiativeK4DD Switzerland
CitationJournal: To Be Published
Title: Human IGF1R with inhibitor 47
Authors: Dreyer, M.K. / Wang, J. / Elkins, J.M.
History
DepositionJul 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Insulin-like growth factor 1 receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3275
Polymers36,7161
Non-polymers6114
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-17 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.537, 69.537, 140.442
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Insulin-like growth factor 1 receptor beta chain


Mass: 36715.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1R / Plasmid: pFB-CT10HF-LIC / Cell (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08069
#2: Chemical ChemComp-IC2 / 5,5-dimethyl-1-(1H-pyrrolo[2,3-b]pyridin-3-ylmethyl)-3-[4-(trifluoromethylsulfanyl)phenyl]imidazolidine-2,4-dione


Mass: 434.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17F3N4O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M HEPES pH 7.5-8.5, 9-12 % PEG3350, 5 mM CoCl2, 5 mM CdCl2, 5 mM MgCl2, and 5 mM NiCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.23→17562 Å / Num. obs: 223284 / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.5
Reflection shellResolution: 2.23→2.35 Å / Rmerge(I) obs: 1.3 / Num. unique obs: 2485

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→21.134 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.898 / SU B: 10.963 / SU ML: 0.149 / Cross valid method: FREE R-VALUE / ESU R: 0.249 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2526 872 4.992 %
Rwork0.198 16595 -
all0.201 --
obs-17467 99.806 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 68.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å2-0 Å2
2--0.53 Å2-0 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.23→21.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 33 57 2276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132271
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152164
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.6663066
X-RAY DIFFRACTIONr_angle_other_deg1.2871.5854965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7655274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75421.653121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67515415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0261518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02519
X-RAY DIFFRACTIONr_nbd_refined0.2160.2471
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22021
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21054
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21084
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.273
X-RAY DIFFRACTIONr_metal_ion_refined0.0720.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.218
X-RAY DIFFRACTIONr_nbd_other0.2470.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3180.210
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0110.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.6350.22
X-RAY DIFFRACTIONr_mcbond_it2.1793.2041096
X-RAY DIFFRACTIONr_mcbond_other2.1663.21095
X-RAY DIFFRACTIONr_mcangle_it3.4994.7931367
X-RAY DIFFRACTIONr_mcangle_other3.4994.7981368
X-RAY DIFFRACTIONr_scbond_it2.6263.5181175
X-RAY DIFFRACTIONr_scbond_other2.6133.5131170
X-RAY DIFFRACTIONr_scangle_it4.1235.1511698
X-RAY DIFFRACTIONr_scangle_other4.1265.1431690
X-RAY DIFFRACTIONr_lrange_it7.61536.7712532
X-RAY DIFFRACTIONr_lrange_other7.60936.6062521
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.23-2.2870.316560.27211890.27412450.8220.8391000.244
2.287-2.3490.278660.25911530.2612190.8450.8681000.224
2.349-2.4160.327510.24511380.24911890.8740.881000.211
2.416-2.490.31660.21910830.22511490.9020.9051000.186
2.49-2.570.256610.18510640.18911250.9190.9371000.15
2.57-2.6590.22550.19110310.19210860.9310.941000.157
2.659-2.7580.218390.16210130.16410520.9550.9561000.128
2.758-2.8680.215670.1639490.16710160.9440.9561000.129
2.868-2.9930.178620.169200.1629820.9530.961000.132
2.993-3.1360.201400.1678950.1689350.9560.9581000.136
3.136-3.3020.211370.1698690.1719060.9480.9571000.139
3.302-3.4970.222480.1648010.1678490.9480.9631000.14
3.497-3.7310.197460.1697600.178060.9560.9641000.149
3.731-4.020.234420.1677120.177540.9350.9671000.155
4.02-4.3870.193310.1826730.1827040.9640.9661000.174
4.387-4.8790.247260.1846250.1876530.9440.96399.69370.176
4.879-5.5840.259260.235520.2325780.9310.9441000.219
5.584-6.7230.326190.2514880.2545070.8910.9241000.25
6.723-9.0610.327220.2274000.2324220.9190.9381000.233
9.061-21.1340.475120.2892800.2972920.8730.9181000.321
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)
17.99781.04212.00586.0898-0.36795.6810.23530.6215-0.6154-0.9291-0.01151.12040.4686-1.2078-0.22380.5486-0.163-0.09140.71310.01670.4247-45.676-8.866-13.739
24.9919-0.1956-1.10835.344-0.34324.68980.17850.06360.17030.1184-0.1122-0.1139-0.1901-0.2555-0.06630.2388-0.0001-0.00950.0770.02110.0125-24.1446.088-18.712
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AAAA986 - 108014 - 108
2X-RAY DIFFRACTION2AAAA1081 - 1270109 - 298

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