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- PDB-3f5p: Complex Structure of Insulin-like Growth Factor Receptor and 3-Cy... -

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Basic information

Entry
Database: PDB / ID: 3f5p
TitleComplex Structure of Insulin-like Growth Factor Receptor and 3-Cyanoquinoline Inhibitor
ComponentsInsulin-like growth factor 1 receptor
KeywordsTRANSFERASE / IGF-1R / protein-inhibitor complex / tyrosine kinase / ATP-binding / Cleavage on pair of basic residues / Disease mutation / Glycoprotein / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


protein kinase complex / insulin-like growth factor receptor activity / insulin-like growth factor binding / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / protein transporter activity / IRS-related events triggered by IGF1R / transcytosis / insulin receptor complex / insulin-like growth factor I binding / positive regulation of protein-containing complex disassembly ...protein kinase complex / insulin-like growth factor receptor activity / insulin-like growth factor binding / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / protein transporter activity / IRS-related events triggered by IGF1R / transcytosis / insulin receptor complex / insulin-like growth factor I binding / positive regulation of protein-containing complex disassembly / insulin receptor activity / alphav-beta3 integrin-IGF-1-IGF1R complex / regulation of JNK cascade / dendritic spine maintenance / peptidyl-tyrosine autophosphorylation / insulin binding / amyloid-beta clearance / Respiratory syncytial virus (RSV) attachment and entry / insulin receptor substrate binding / SHC-related events triggered by IGF1R / phosphatidylinositol 3-kinase binding / negative regulation of MAPK cascade / insulin-like growth factor receptor signaling pathway / insulin receptor binding / cellular response to glucose stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor protein-tyrosine kinase / cellular response to amyloid-beta / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / protein autophosphorylation / protein tyrosine kinase activity / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of MAPK cascade / immune response / cilium / positive regulation of cell migration / axon / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / negative regulation of apoptotic process / nucleolus / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-741 / Insulin-like growth factor 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsXu, W. / Miller, L.M. / Mayer, S.C. / Berger, D.M. / Boschelli, D.H. / Boschelli, F.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Lead identification to generate 3-cyanoquinoline inhibitors of insulin-like growth factor receptor (IGF-1R) for potential use in cancer treatment
Authors: Miller, L.M. / Mayer, S.C. / Berger, D.M. / Boschelli, D.H. / Boschelli, F. / Di, L. / Du, X. / Dutia, M. / Floyd, M.B. / Johnson, M. / Kenny, C.H. / Krishnamurthy, G. / Moy, F. / Petusky, S. ...Authors: Miller, L.M. / Mayer, S.C. / Berger, D.M. / Boschelli, D.H. / Boschelli, F. / Di, L. / Du, X. / Dutia, M. / Floyd, M.B. / Johnson, M. / Kenny, C.H. / Krishnamurthy, G. / Moy, F. / Petusky, S. / Tkach, D. / Torres, N. / Wu, B. / Xu, W.
#1: Journal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Lead identification to generate isoquinolinedione inhibitors of insulin-like growth factor receptor (IGF-1R) for potential use in cancer treatment
Authors: Mayer, S.C. / Banker, A.L. / Boschelli, F. / Di, L. / Johnson, M. / Kenny, C.H. / Krishnamurthy, G. / Kutterer, K. / Moy, F. / Petusky, S. / Ravi, M. / Tkach, D. / Tsou, H.R. / Xu, W.
History
DepositionNov 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 17, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Nov 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
E: Insulin-like growth factor 1 receptor
F: Insulin-like growth factor 1 receptor
G: Insulin-like growth factor 1 receptor
H: Insulin-like growth factor 1 receptor
I: Insulin-like growth factor 1 receptor
J: Insulin-like growth factor 1 receptor
K: Insulin-like growth factor 1 receptor
M: Insulin-like growth factor 1 receptor
L: Insulin-like growth factor 1 receptor
R: Insulin-like growth factor 1 receptor
S: Insulin-like growth factor 1 receptor
T: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)574,32432
Polymers565,47416
Non-polymers8,84916
Water2,990166
1
A: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
H: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
9
I: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
10
J: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
11
K: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
12
M: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
13
L: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
14
R: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
15
S: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
16
T: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,3421
Non-polymers5531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
17
C: Insulin-like growth factor 1 receptor
D: Insulin-like growth factor 1 receptor
G: Insulin-like growth factor 1 receptor
H: Insulin-like growth factor 1 receptor
hetero molecules

K: Insulin-like growth factor 1 receptor
M: Insulin-like growth factor 1 receptor
L: Insulin-like growth factor 1 receptor
R: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,16216
Polymers282,7378
Non-polymers4,4258
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area15210 Å2
ΔGint-93 kcal/mol
Surface area104840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.340, 137.020, 178.990
Angle α, β, γ (deg.)90.00, 110.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Insulin-like growth factor 1 receptor / Insulin-like growth factor I receptor / IGF-I receptor / CD221 antigen


Mass: 35342.145 Da / Num. of mol.: 16 / Fragment: IGF-1R Kinase Domain, UNP residues 981-1286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1R / Cell (production host): cancer cell / Production host: Homo sapiens (human)
References: UniProt: P08069, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-741 / 4-[[3-chloro-4-(1-methylimidazol-2-yl)sulfanyl-phenyl]amino]-7-[3-(2-hydroxyethyl-methyl-amino)propoxy]-6-methoxy-quinoline-3-carbonitrile


Mass: 553.076 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C27H29ClN6O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH8.5, 2M NaCl, 14% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 143 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 137596 / Num. obs: 133523 / % possible obs: 97.04 % / Rmerge(I) obs: 0.095
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.67 / % possible all: 89.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZM3

2zm3


Resolution: 2.9→19.986 Å / SU ML: 0.44 / Isotropic thermal model: isotropic / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.258 6713 5.03 %random
Rwork0.2097 ---
obs0.2122 133523 97.04 %-
all-137652 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.778 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 45.13 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38312 0 608 166 39086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_deg1.108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8976-2.93040.33971720.28553675X-RAY DIFFRACTION84
2.9304-2.96480.32361850.28553889X-RAY DIFFRACTION90
2.9648-3.00080.32362250.2863903X-RAY DIFFRACTION91
3.0008-3.03870.33622340.28744007X-RAY DIFFRACTION93
3.0387-3.07850.36462530.28633994X-RAY DIFFRACTION93
3.0785-3.12050.35422280.27634119X-RAY DIFFRACTION95
3.1205-3.1650.33892080.26724138X-RAY DIFFRACTION96
3.165-3.2120.32542100.25154194X-RAY DIFFRACTION96
3.212-3.2620.31732000.26284229X-RAY DIFFRACTION96
3.262-3.31520.34472270.25254168X-RAY DIFFRACTION97
3.3152-3.37210.26412420.24294206X-RAY DIFFRACTION97
3.3721-3.43320.30932200.23734246X-RAY DIFFRACTION97
3.4332-3.49880.25232340.20624228X-RAY DIFFRACTION98
3.4988-3.56990.26612350.20264292X-RAY DIFFRACTION99
3.5699-3.6470.26342530.20514293X-RAY DIFFRACTION99
3.647-3.73130.26032300.20694300X-RAY DIFFRACTION99
3.7313-3.8240.2622020.20374358X-RAY DIFFRACTION99
3.824-3.92670.24072470.19094264X-RAY DIFFRACTION99
3.9267-4.04130.24322140.17514362X-RAY DIFFRACTION99
4.0413-4.17060.21252220.17024343X-RAY DIFFRACTION99
4.1706-4.31820.21372230.17514303X-RAY DIFFRACTION99
4.3182-4.48920.19892390.15654335X-RAY DIFFRACTION100
4.4892-4.6910.21512260.17814327X-RAY DIFFRACTION99
4.691-4.93480.22312360.18644340X-RAY DIFFRACTION99
4.9348-5.23880.20832050.18194406X-RAY DIFFRACTION100
5.2388-5.63490.24352060.19044369X-RAY DIFFRACTION99
5.6349-6.18660.23942590.19114326X-RAY DIFFRACTION99
6.1866-7.04730.22132230.17894364X-RAY DIFFRACTION100
7.0473-8.75290.18962260.16244413X-RAY DIFFRACTION100
8.7529-19.98630.20712290.18764419X-RAY DIFFRACTION99

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