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- PDB-8pym: Human IGF1R with inhibitor 54 -

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Basic information

Entry
Database: PDB / ID: 8pym
TitleHuman IGF1R with inhibitor 54
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 / positive regulation of steroid hormone biosynthetic process / protein kinase complex / protein transporter activity / insulin-like growth factor binding / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / positive regulation of steroid hormone biosynthetic process / protein kinase complex / protein transporter activity / insulin-like growth factor binding / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / 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 / cellular response to testosterone stimulus / insulin receptor complex / insulin-like growth factor I binding / transcytosis / negative regulation of hepatocyte apoptotic process / positive regulation of protein-containing complex disassembly / regulation of JNK cascade / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / dendritic spine maintenance / insulin binding / response to L-glutamate / cellular response to insulin-like growth factor stimulus / establishment of cell polarity / positive regulation of axon regeneration / positive regulation of cytokinesis / positive regulation of osteoblast proliferation / amyloid-beta clearance / Respiratory syncytial virus (RSV) attachment and entry / insulin receptor substrate binding / cellular response to angiotensin / response to vitamin E / G-protein alpha-subunit binding / phosphatidylinositol 3-kinase binding / SHC-related events triggered by IGF1R / negative regulation of MAPK cascade / peptidyl-tyrosine autophosphorylation / estrous cycle / cellular response to transforming growth factor beta stimulus / T-tubule / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cerebellum development / axonogenesis / cellular response to dexamethasone stimulus / insulin-like growth factor receptor signaling pathway / hippocampus development / response to nicotine / positive regulation of smooth muscle cell proliferation / cellular response to estradiol stimulus / insulin receptor binding / cellular response to glucose stimulus / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / GPI-linked ephrin receptor activity / transmembrane-ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / 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 / protein autophosphorylation / response to ethanol / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / 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-IED / NICKEL (II) ION / Insulin-like growth factor 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.652 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 54
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)37,3224
Polymers36,7161
Non-polymers6063
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.350, 69.350, 142.850
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 line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08069
#2: Chemical ChemComp-IED / 5,5-dimethyl-1-(1H-pyrrolo[2,3-b]pyridin-4-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.: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
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: X06SA / 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: 2.65→71.43 Å / Num. obs: 10559 / % possible obs: 98.6 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 12
Reflection shellResolution: 2.65→2.66 Å / Rmerge(I) obs: 1.81 / Num. unique obs: 111

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.652→62.387 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.82 / SU B: 29.767 / SU ML: 0.321 / Cross valid method: FREE R-VALUE / ESU R: 1.22 / ESU R Free: 0.407
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3086 486 4.721 %
Rwork0.2364 9809 -
all0.24 --
obs-10295 96.161 %
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: 41.529 Å2
Baniso -1Baniso -2Baniso -3
1-2.537 Å2-0 Å2-0 Å2
2--2.537 Å2-0 Å2
3----5.074 Å2
Refinement stepCycle: LAST / Resolution: 2.652→62.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 32 47 2292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132291
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152175
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.6663095
X-RAY DIFFRACTIONr_angle_other_deg1.2151.5844995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9875276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80321.917120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.63815413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7191517
X-RAY DIFFRACTIONr_chiral_restr0.0660.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022543
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02515
X-RAY DIFFRACTIONr_nbd_refined0.2140.2512
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.22140
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21091
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0080.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2560.26
X-RAY DIFFRACTIONr_nbd_other0.250.219
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1910.25
X-RAY DIFFRACTIONr_mcbond_it0.6551.6421110
X-RAY DIFFRACTIONr_mcbond_other0.6551.6391109
X-RAY DIFFRACTIONr_mcangle_it1.1942.4531384
X-RAY DIFFRACTIONr_mcangle_other1.1932.4561385
X-RAY DIFFRACTIONr_scbond_it0.5791.7481181
X-RAY DIFFRACTIONr_scbond_other0.5791.7491182
X-RAY DIFFRACTIONr_scangle_it1.0442.5911711
X-RAY DIFFRACTIONr_scangle_other1.0432.5921712
X-RAY DIFFRACTIONr_lrange_it2.89719.1042591
X-RAY DIFFRACTIONr_lrange_other2.86119.0682584
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
2.652-2.7210.496250.5296310.5277680.4630.43385.41670.512
2.721-2.7950.364350.3087140.3117500.580.59699.86670.283
2.795-2.8760.386330.3036960.3077290.6870.7631000.271
2.876-2.9640.364290.2616700.2666990.8180.8661000.227
2.964-3.0610.314290.2376690.2416980.8810.8981000.205
3.061-3.1690.277300.2246440.2266740.860.9171000.195
3.169-3.2880.293250.2276180.236430.8770.9131000.195
3.288-3.4220.305330.2455690.2486140.8860.998.04560.212
3.422-3.5730.31180.2815030.2826060.8890.985.97360.249
3.573-3.7470.304260.3084990.3085660.8350.89792.75620.271
3.747-3.9490.267240.223790.2235600.9320.92871.96430.182
3.949-4.1870.428110.1815060.1855180.8780.94899.8070.154
4.187-4.4750.281270.1624760.1675030.9070.9521000.136
4.475-4.8320.313260.1734350.184610.9120.9551000.144
4.832-5.290.305290.1654130.1734420.940.9641000.143
5.29-5.9090.214250.1833650.1853900.9610.9561000.156
5.909-6.8130.278220.2033360.2073580.9170.9451000.174
6.813-8.3190.23170.192890.1923060.9330.9511000.168
8.319-11.6620.34190.1762440.1812530.9160.9631000.169
11.662-62.3870.327130.2911500.2941630.8970.9311000.282
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)
13.14130.88432.01223.4497-0.67474.91080.01430.1146-0.1572-0.43130.08170.66340.7528-0.8236-0.0960.321-0.1814-0.01770.5033-0.00140.517-44.91-9.272-14.24
22.65880.1797-0.34282.2763-0.69593.61980.0481-0.07960.16260.0555-0.0589-0.0164-0.2258-0.08140.01080.07130.0062-0.02260.01110.0190.1793-24.2776.512-18.927
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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