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- PDB-5j9x: HSP90 in complex with N-Butyl-5-[4-(2-fluoro-phenyl)-5-oxo-4,5-di... -

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Basic information

Entry
Database: PDB / ID: 5j9x
TitleHSP90 in complex with N-Butyl-5-[4-(2-fluoro-phenyl)-5-oxo-4,5-dihydro-1H-[1,2,4]triazol-3-yl]-2,4-dihydroxy-N-methyl-benzamide
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE / Inhibitor
Function / homology
Function and homology information


sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy ...sperm mitochondrial sheath / sulfonylurea receptor binding / 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 / protein insertion into mitochondrial outer membrane / 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 / TPR domain binding / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / PIWI-interacting RNA (piRNA) biogenesis / dendritic growth cone / Sema3A PAK dependent Axon repulsion / protein unfolding / positive regulation of cell size / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / enzyme-substrate adaptor activity / skeletal muscle contraction / HSF1 activation / regulation of protein-containing complex assembly / telomere maintenance via telomerase / regulation of postsynaptic membrane neurotransmitter receptor levels / Attenuation phase / chaperone-mediated protein complex assembly / neurofibrillary tangle assembly / axonal growth cone / 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 / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / nitric-oxide synthase regulator activity / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / activation of innate immune response / Anchoring of the basal body to the plasma membrane / lysosomal lumen / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cold / ESR-mediated signaling / Constitutive Signaling by Overexpressed ERBB2 / protein tyrosine kinase binding / AURKA Activation by TPX2 / VEGFR2 mediated vascular permeability / ATP-dependent protein folding chaperone / response to cocaine / Signaling by ERBB2 TMD/JMD mutants / brush border membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / Regulation of necroptotic cell death / tau protein binding / VEGFA-VEGFR2 Pathway / histone deacetylase binding / positive regulation of protein import into nucleus / Downregulation of ERBB2 signaling / response to estrogen / Chaperone Mediated Autophagy / positive regulation of protein catabolic process / neuron migration / Aggrephagy / MHC class II protein complex binding / disordered domain specific binding / The role of GTSE1 in G2/M progression after G2 checkpoint
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6GC / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAmaral, M. / Matias, P.
Funding support1items
OrganizationGrant numberCountry
IMI-K4DD155366
CitationJournal: Nat Commun / Year: 2017
Title: Protein conformational flexibility modulates kinetics and thermodynamics of drug binding.
Authors: Amaral, M. / Kokh, D.B. / Bomke, J. / Wegener, A. / Buchstaller, H.P. / Eggenweiler, H.M. / Matias, P. / Sirrenberg, C. / Wade, R.C. / Frech, M.
History
DepositionApr 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8063
Polymers25,3271
Non-polymers4792
Water3,045169
1
A: Heat shock protein HSP 90-alpha
hetero molecules

A: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6126
Polymers50,6552
Non-polymers9574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)67.894, 91.334, 98.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Heat shock protein HSP 90-alpha / Heat shock 86 kDa / HSP86 / Lipopolysaccharide-associated protein 2 / LPS-associated protein 2 / ...Heat shock 86 kDa / HSP86 / Lipopolysaccharide-associated protein 2 / LPS-associated protein 2 / Renal carcinoma antigen NY-REN-38


Mass: 25327.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Production host: Escherichia coli (E. coli) / References: UniProt: P07900
#2: Chemical ChemComp-6GC / N-butyl-5-[4-(2-fluorophenyl)-5-oxo-4,5-dihydro-1H-1,2,4-triazol-3-yl]-2,4-dihydroxy-N-methylbenzamide


Mass: 400.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21FN4O4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium fluoride 0.1 M Bis Tris propane pH 8.5 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→45.67 Å / Num. obs: 28122 / % possible obs: 97.5 % / Redundancy: 5.98 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 21.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6.63 % / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YES

1yes


Resolution: 1.8→36.631 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.67
RfactorNum. reflection% reflection
Rfree0.2344 1301 5.01 %
Rwork0.1858 --
obs0.1882 25976 89.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→36.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 33 169 1838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121696
X-RAY DIFFRACTIONf_angle_d1.4162289
X-RAY DIFFRACTIONf_dihedral_angle_d13.3021010
X-RAY DIFFRACTIONf_chiral_restr0.057258
X-RAY DIFFRACTIONf_plane_restr0.007292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.87210.53951470.47012794X-RAY DIFFRACTION99
1.8721-1.95730.5797740.5611424X-RAY DIFFRACTION51
1.9573-2.06050.44591470.35452785X-RAY DIFFRACTION92
2.0605-2.18960.31521380.29392598X-RAY DIFFRACTION86
2.1896-2.35860.28041510.22832851X-RAY DIFFRACTION94
2.3586-2.59590.23031600.18153049X-RAY DIFFRACTION100
2.5959-2.97140.2481560.18162960X-RAY DIFFRACTION98
2.9714-3.74310.21721610.15473046X-RAY DIFFRACTION99
3.7431-36.6390.16711670.13663168X-RAY DIFFRACTION99
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)
11.4294-0.1724-0.00490.86870.2290.4790.0754-0.12260.01540.04210.1949-0.08220.01490.3123-0.00020.25970.0506-0.02870.3764-0.02820.294713.179327.616-18.0479
21.4622-0.2416-0.46711.84850.74511.7640.03870.26510.0641-0.295-0.10920.1776-0.0229-0.1805-0.00050.2250.0123-0.04750.2698-0.03050.253-5.5733.7076-24.7801
31.1732-0.76250.32520.8643-0.54321.1586-0.024-0.0031.20990.0425-0.0755-0.3078-0.09260.9463-0.12220.248-0.0544-0.01050.4643-0.09590.485112.677539.4751-15.0543
41.4921-0.145-1.32011.32280.51131.2679-0.06150.3947-0.2114-0.1565-0.02160.01940.1846-0.0528-0.00040.23010.0156-0.01270.3009-0.06130.28291.652325.5733-26.942
50.40640.0210.06540.41640.10650.7992-0.1348-0.485-0.08760.1035-0.00820.06110.2282-0.3352-0.00470.3396-0.00060.00990.33340.02870.2762-6.025925.7917-6.9084
60.1853-0.173-0.01591.057-1.3222.2836-0.1269-0.5806-0.01180.81430.17280.1704-0.6892-0.48030.00140.24920.00570.00250.44830.01210.3644-13.04433.199-15.5185
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 105 )
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 136 )
4X-RAY DIFFRACTION4chain 'A' and (resid 137 through 190 )
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 210 )
6X-RAY DIFFRACTION6chain 'A' and (resid 211 through 223 )

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