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- PDB-3lw0: IGF-1RK in complex with ligand MSC1609119A-1 -

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Basic information

Entry
Database: PDB / ID: 3lw0
TitleIGF-1RK in complex with ligand MSC1609119A-1
ComponentsInsulin-like growth factor 1 receptor
KeywordsTRANSFERASE / PROTEIN 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 / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / protein transporter activity / 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 / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / protein transporter activity / 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 / cellular response to angiotensin / positive regulation of protein-containing complex disassembly / dendritic spine maintenance / cellular response to insulin-like growth factor stimulus / response to L-glutamate / insulin binding / negative regulation of MAPK cascade / establishment of cell polarity / positive regulation of axon regeneration / amyloid-beta clearance / positive regulation of osteoblast proliferation / positive regulation of cytokinesis / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / insulin receptor substrate binding / estrous cycle / 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 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / insulin-like growth factor receptor signaling pathway / caveola / cellular response to estradiol stimulus / hippocampus development / cellular response to glucose stimulus / positive regulation of smooth muscle cell proliferation / response to nicotine / 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 / positive regulation of MAPK cascade / protein autophosphorylation / 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 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-CCX / Insulin-like growth factor 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsGraedler, U. / Heinrich, T. / Boettcher, H. / Blaukat, A. / Shutes, A. / Askew, B.
CitationJournal: Acs Med.Chem.Lett. / Year: 2010
Title: Allosteric IGF-1R Inhibitors.
Authors: Heinrich, T. / Gradler, U. / Bottcher, H. / Blaukat, A. / Shutes, A.
History
DepositionFeb 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2019Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)142,33214
Polymers138,4314
Non-polymers3,90110
Water18,8981049
1
A: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5373
Polymers34,6081
Non-polymers9292
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)35,6294
Polymers34,6081
Non-polymers1,0213
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)35,6294
Polymers34,6081
Non-polymers1,0213
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)35,5373
Polymers34,6081
Non-polymers9292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)189.346, 189.346, 115.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Insulin-like growth factor 1 receptor / IGF-1 RECEPTOR KINASE / Insulin-like growth factor I receptor / IGF-I receptor / Insulin-like ...IGF-1 RECEPTOR KINASE / 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: 34607.758 Da / Num. of mol.: 4 / Fragment: PROTEIN KINASE, UNP residues 983-1286 / Mutation: E1097A, E1099A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1R / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P08069, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-CCX / 3-cyano-N-{1-[4-(5-cyano-1H-indol-3-yl)butyl]piperidin-4-yl}-1H-indole-7-carboxamide / 3-Cyano-1H-indole-7-carboxylic acid {1-[4-(5-cyano-1H-indol-3-yl)-butyl]-piperidin-4-yl}-amide


Mass: 464.562 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C28H28N6O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1049 / 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: 2.92 Å3/Da / Density % sol: 57.95 % / Description: NONE
Crystal growpH: 0 / Details: pH 0.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→20 Å / Num. obs: 9614 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.116 / Rsym value: 0.103 / Net I/σ(I): 11.72
Reflection shellResolution: 1.79→1.87 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 4.2 / Num. unique all: 9614 / Rsym value: 0.468 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JQH

1jqh


Resolution: 1.79→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.185 4956 3.4 %RANDOM
Rwork0.157 ---
obs-9614 --
Displacement parametersBiso mean: 12.868 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å20 Å2
2---0.11 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.79→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9368 0 292 1049 10709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229995
X-RAY DIFFRACTIONr_bond_other_d0.0010.029017
X-RAY DIFFRACTIONr_angle_refined_deg1.231.99113522
X-RAY DIFFRACTIONr_angle_other_deg1.205320990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70451208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25824.123456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.439151738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5791568
X-RAY DIFFRACTIONr_chiral_restr0.0790.21425
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211046
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022050
X-RAY DIFFRACTIONr_nbd_refined0.2050.21919
X-RAY DIFFRACTIONr_nbd_other0.1860.28409
X-RAY DIFFRACTIONr_nbtor_refined0.1740.24885
X-RAY DIFFRACTIONr_nbtor_other0.0710.24964
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2691
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0470.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0750.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.240
X-RAY DIFFRACTIONr_mcbond_it1.7727732
X-RAY DIFFRACTIONr_mcbond_other0.2422416
X-RAY DIFFRACTIONr_mcangle_it1.90939650
X-RAY DIFFRACTIONr_scbond_it3.15144879
X-RAY DIFFRACTIONr_scangle_it4.48263872
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)
12.8345-0.45970.31445.874-0.67961.58710.05890.01590.4580.01050.03280.4253-0.0767-0.2392-0.0917-0.046-0.01190.0277-0.04950.03180.097-3.098-14.96-62.207
22.27620.1882-0.56411.4116-0.44321.9242-0.01320.02120.051-0.04090.02850.01280.0081-0.0704-0.0154-0.09770.0045-0.0145-0.1360.0037-0.1375-3.992-37.655-50.315
32.11820.69410.36412.4802-0.72995.62920.1376-0.124-0.25760.3846-0.1260.00060.4043-0.1822-0.01160.0934-0.0528-0.0342-0.0215-0.0063-0.0607-9.112-52.9626.239
41.39470.0108-0.27952.52130.58161.6976-0.0036-0.0202-0.04530.0533-0.04070.0350.0142-0.04620.0442-0.12710.00560.0046-0.09670.008-0.1439-6.386-55.579-19.106
55.56761.04390.5841.77040.60432.97510.0625-0.16220.06620.1713-0.20560.2946-0.0462-0.50370.1432-0.0383-0.0142-0.00560.0654-0.0815-0.025-35.998-27.656-8.639
61.44730.0042-0.31332.47880.62091.68990.02520.0038-0.0240.0762-0.02240.03540.0089-0.046-0.0027-0.1296-0.0122-0.0104-0.11960.0153-0.1204-16.721-12.418-1.245
73.45841.50361.62383.20120.25243.5616-0.1270.35580.1548-0.44810.1810.13550.108-0.1586-0.0540.0224-0.0903-0.02810.00950.0321-0.02595.382-40.997-91.125
82.17970.1894-0.57011.3447-0.44342.04890.03170.04530.0647-0.0334-0.00830.03650.004-0.0458-0.0235-0.13170.0019-0.0157-0.1214-0.0129-0.115628.222-30.914-85.083
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A983 - 1081
2X-RAY DIFFRACTION2A1082 - 1286
3X-RAY DIFFRACTION3B983 - 1081
4X-RAY DIFFRACTION4B1082 - 1286
5X-RAY DIFFRACTION5C983 - 1081
6X-RAY DIFFRACTION6C1082 - 1286
7X-RAY DIFFRACTION7D983 - 1081
8X-RAY DIFFRACTION8D1082 - 1286

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