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- PDB-8pyj: Human IGF1R with inhibitor 8 -

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Basic information

Entry
Database: PDB / ID: 8pyj
TitleHuman IGF1R with inhibitor 8
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 / 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 / cellular response to testosterone stimulus / negative regulation of hepatocyte apoptotic process / 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 / dendritic spine maintenance / response to L-glutamate / 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 / cellular response to dexamethasone stimulus / cerebellum development / 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 / cellular response to glucose stimulus / hippocampus development / 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 / 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-IEA / NICKEL (II) ION / Insulin-like growth factor 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 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 8
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)37,4305
Polymers36,7161
Non-polymers7144
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-34 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.300, 69.300, 142.804
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules AAA

#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

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Non-polymers , 5 types, 49 molecules

#2: Chemical ChemComp-IEA / 5,5-dimethyl-1-(quinolin-4-ylmethyl)-3-[4-(trifluoromethylsulfonyl)phenyl]imidazolidine-2,4-dione


Mass: 477.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18F3N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density % sol: 47.32 %
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: Jun 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.69→142.8 Å / Num. obs: 10028 / % possible obs: 97 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 14.3
Reflection shellResolution: 2.69→2.83 Å / Rmerge(I) obs: 1.3 / Num. unique obs: 1456

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.702→49.729 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.819 / SU B: 25.824 / SU ML: 0.286 / Cross valid method: FREE R-VALUE / ESU R: 2.167 / ESU R Free: 0.417
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3024 467 4.777 %
Rwork0.1989 9309 -
all0.204 --
obs-9776 96.563 %
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: 46.011 Å2
Baniso -1Baniso -2Baniso -3
1-2.364 Å2-0 Å2-0 Å2
2--2.364 Å2-0 Å2
3----4.727 Å2
Refinement stepCycle: LAST / Resolution: 2.702→49.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2209 0 36 45 2290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132290
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152173
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.6393095
X-RAY DIFFRACTIONr_angle_other_deg1.2581.5885008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6435275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09721.917120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.97915414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2011517
X-RAY DIFFRACTIONr_chiral_restr0.0750.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022537
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02523
X-RAY DIFFRACTIONr_nbd_refined0.2250.2499
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22083
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21084
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.266
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2940.26
X-RAY DIFFRACTIONr_nbd_other0.2390.222
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0460.24
X-RAY DIFFRACTIONr_mcbond_it1.142.0751106
X-RAY DIFFRACTIONr_mcbond_other1.1142.0741105
X-RAY DIFFRACTIONr_mcangle_it2.0253.11379
X-RAY DIFFRACTIONr_mcangle_other2.0283.1031380
X-RAY DIFFRACTIONr_scbond_it1.1362.2261184
X-RAY DIFFRACTIONr_scbond_other1.1362.2281185
X-RAY DIFFRACTIONr_scangle_it1.9543.2881716
X-RAY DIFFRACTIONr_scangle_other1.9543.291717
X-RAY DIFFRACTIONr_lrange_it4.07723.9832571
X-RAY DIFFRACTIONr_lrange_other4.05323.952566
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
2.702-2.7720.302320.2917040.2927410.8150.82299.32520.264
2.772-2.8480.38340.2446600.2516940.7930.8581000.217
2.848-2.930.322290.2486650.2516940.8570.8791000.22
2.93-3.020.297250.2346400.2376650.8980.8921000.202
3.02-3.1180.29290.2076160.2116450.8620.9111000.17
3.118-3.2270.257300.2056010.2076310.8820.9171000.172
3.227-3.3490.366250.2115870.2166120.8340.9211000.177
3.349-3.4850.255220.2334450.2345930.9120.91378.75210.197
3.485-3.6390.368300.1995380.2075700.8380.92899.64910.17
3.639-3.8160.331200.2114080.2165330.8710.92980.30020.174
3.816-4.0210.232130.2114030.2125230.9520.94479.54110.164
4.021-4.2630.294170.1494830.1535000.9110.9641000.122
4.263-4.5550.263280.1624420.1684700.9230.9551000.134
4.555-4.9160.385210.1594210.1674420.8880.9591000.124
4.916-5.380.253330.1623750.1694080.9520.9641000.131
5.38-6.0060.179220.1563500.1583720.9610.9631000.131
6.006-6.9190.303200.1743210.1823410.9130.9541000.147
6.919-8.4330.242150.1672770.1712920.9190.9531000.142
8.433-11.7580.32390.1732290.1782390.9140.95899.58160.16
11.758-49.7290.479130.31440.3131570.7890.9261000.281
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)
14.28480.53032.41033.486-0.72413.8550.02380.1791-0.3344-0.38010.14780.80650.6131-0.8167-0.17150.3268-0.18520.00620.5373-0.02030.5002-45.049-8.742-14.043
22.92180.1238-0.36032.3555-0.5783.44320.0598-0.04880.17640.022-0.0518-0.0146-0.2354-0.0968-0.0080.0801-0.0045-0.01740.01020.01950.1618-24.3056.615-18.892
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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