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Open data
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Basic information
Entry | Database: PDB / ID: 2ykj | ||||||
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Title | Tricyclic series of Hsp90 inhibitors | ||||||
![]() | HEAT SHOCK PROTEIN HSP 90-ALPHA | ||||||
![]() | CHAPERONE / INHIBITION | ||||||
Function / homology | ![]() sulfonylurea receptor binding / sperm mitochondrial sheath / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy ...sulfonylurea receptor binding / sperm mitochondrial sheath / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / protein insertion into mitochondrial outer membrane / TPR domain binding / dendritic growth cone / Assembly and release of respiratory syncytial virus (RSV) virions / PIWI-interacting RNA (piRNA) biogenesis / non-chaperonin molecular chaperone ATPase / Sema3A PAK dependent Axon repulsion / protein unfolding / regulation of protein ubiquitination / positive regulation of cell size / HSF1-dependent transactivation / response to unfolded protein / enzyme-substrate adaptor activity / HSF1 activation / skeletal muscle contraction / regulation of protein-containing complex assembly / axonal growth cone / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / neurofibrillary tangle assembly / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / eNOS activation / nitric oxide metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / DNA polymerase binding / positive regulation of defense response to virus by host / response to salt stress / Signaling by ERBB2 / positive regulation of telomere maintenance via telomerase / cardiac muscle cell apoptotic process / positive regulation of cardiac muscle contraction / endocytic vesicle lumen / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / activation of innate immune response / Recruitment of NuMA to mitotic centrosomes / lysosomal lumen / Anchoring of the basal body to the plasma membrane / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / ESR-mediated signaling / protein tyrosine kinase binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cold / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / VEGFR2 mediated vascular permeability / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / Regulation of actin dynamics for phagocytic cup formation / cellular response to virus / Regulation of necroptotic cell death / tau protein binding / positive regulation of protein import into nucleus / VEGFA-VEGFR2 Pathway / response to estrogen / Downregulation of ERBB2 signaling / histone deacetylase binding / neuron migration / Chaperone Mediated Autophagy / positive regulation of protein catabolic process / Aggrephagy / positive regulation of nitric oxide biosynthetic process / MHC class II protein complex binding / disordered domain specific binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Dupuy, A. / Vallee, F. | ||||||
![]() | ![]() Title: Tricyclic Series of Heat Shock Protein 90 (Hsp90) Inhibitors Part I: Discovery of Tricyclic Imidazo[4,5-C]Pyridines as Potent Inhibitors of the Hsp90 Molecular Chaperone. Authors: Vallee, F. / Carrez, C. / Pilorge, F. / Dupuy, A. / Parent, A. / Bertin, L. / Thompson, F. / Ferrari, P. / Fassy, F. / Lamberton, A. / Thomas, A. / Arrebola, R. / Guerif, S. / Rohaut, A. / ...Authors: Vallee, F. / Carrez, C. / Pilorge, F. / Dupuy, A. / Parent, A. / Bertin, L. / Thompson, F. / Ferrari, P. / Fassy, F. / Lamberton, A. / Thomas, A. / Arrebola, R. / Guerif, S. / Rohaut, A. / Certal, V. / Ruxer, J.M. / Delorme, C. / Jouanen, A. / Dumas, J. / Grepin, C. / Combeau, C. / Goulaouic, H. / Dereu, N. / Mikol, V. / Mailliet, P. / Minoux, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.3 KB | Display | ![]() |
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PDB format | ![]() | 46.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1023.5 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yjwC ![]() 2yjxC ![]() 2yk2C ![]() 2yk9C ![]() 2ykbC ![]() 2ykcC ![]() 2ykeC ![]() 2ykiC ![]() 2cdd C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 23361.486 Da / Num. of mol.: 1 / Fragment: N-DOMAIN, RESIDUES 18-233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-YKJ / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | 2-AMINO-N-[4-(3H-IMIDAZO[4, 5-C]PYRIDIN-2-YL)-9H-FLUOREN-9-YL]-ISONICOTINAMIDE (YKJ): ALTERNATIVE ...2-AMINO-N-[4-(3H-IMIDAZO[4, 5-C]PYRIDIN-2-YL)-9H-FLUOREN-9-YL]-ISONICOTIN |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.5 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 6, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→67.42 Å / Num. obs: 52242 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.08 |
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Processing
Software | Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER / Resolution: 1.46→67.42 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Refinement step | Cycle: LAST / Resolution: 1.46→67.42 Å
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Refine LS restraints |
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