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- PDB-5in9: Crystal structure of Grp94 bound to methyl 3-chloro-2-(2-(1-((5-c... -

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Basic information

Entry
Database: PDB / ID: 5in9
TitleCrystal structure of Grp94 bound to methyl 3-chloro-2-(2-(1-((5-chlorofuran-2-yl)methyl)-1H-imidazol-2-yl)ethyl)-4,6-dihydroxybenzoate, an inhibitor based on the BnIm and Radamide scaffolds.
ComponentsEndoplasmin
KeywordsCHAPERONE/INHIBITOR / cation-pi interaction / BnIm and Radamide scaffold-based inhibitor / ATP binding site / CHAPERONE-INHIBITOR complex
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / unfolded protein binding ...Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / unfolded protein binding / melanosome / protein folding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding
Similarity search - Function
Endoplasmic reticulum targeting sequence. / 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 ...Endoplasmic reticulum targeting sequence. / 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-6C0 / TRIETHYLENE GLYCOL / Endoplasmin
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLieberman, R.L. / Huard, D.J.E. / Kizziah, J.L.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Development of Glucose Regulated Protein 94-Selective Inhibitors Based on the BnIm and Radamide Scaffold.
Authors: Crowley, V.M. / Khandelwal, A. / Mishra, S. / Stothert, A.R. / Huard, D.J. / Zhao, J. / Muth, A. / Duerfeldt, A.S. / Kizziah, J.L. / Lieberman, R.L. / Dickey, C.A. / Blagg, B.S.
History
DepositionMar 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Data collection
Revision 1.2Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoplasmin
B: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,54518
Polymers52,3752
Non-polymers2,17016
Water1,13563
1
A: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,48611
Polymers26,1881
Non-polymers1,29810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint2 kcal/mol
Surface area11020 Å2
MethodPISA
2
B: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0597
Polymers26,1881
Non-polymers8726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-1 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.020, 65.650, 95.860
Angle α, β, γ (deg.)90.00, 92.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endoplasmin / 94 kDa glucose-regulated protein / GRP-94 / Heat shock protein 90 kDa beta member 1


Mass: 26187.615 Da / Num. of mol.: 2 / Fragment: residues 69-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: HSP90B1, GRP94, TRA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41148
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-6C0 / methyl 3-chloro-2-(2-{1-[(5-chlorofuran-2-yl)methyl]-1H-imidazol-2-yl}ethyl)-4,6-dihydroxybenzoate


Mass: 411.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H16Cl2N2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystals were grown in 35% PEG 400, 100 mM Tris pH 7.5, 120 mM magnesium chloride. Crystals were harvested and soaked in mother liquor containing 10 mM inhibitor. Glycerol was added and ...Details: Crystals were grown in 35% PEG 400, 100 mM Tris pH 7.5, 120 mM magnesium chloride. Crystals were harvested and soaked in mother liquor containing 10 mM inhibitor. Glycerol was added and crystals were subsequently cryo-cooled with liquid nitrogen

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→47.9 Å / Num. obs: 16605 / % possible obs: 100 % / Redundancy: 7.6 % / Net I/σ(I): 22.93

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GFD

2gfd


Resolution: 2.6→47.868 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.81
RfactorNum. reflection% reflection
Rfree0.2477 3210 9.96 %
Rwork0.1755 --
obs0.1827 32229 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 142 63 3672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093649
X-RAY DIFFRACTIONf_angle_d1.2954896
X-RAY DIFFRACTIONf_dihedral_angle_d17.651340
X-RAY DIFFRACTIONf_chiral_restr0.046553
X-RAY DIFFRACTIONf_plane_restr0.005603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6002-2.6390.31811560.24151297X-RAY DIFFRACTION100
2.639-2.68020.32841440.22321242X-RAY DIFFRACTION100
2.6802-2.72410.27571390.22711257X-RAY DIFFRACTION100
2.7241-2.77110.28991260.20551265X-RAY DIFFRACTION100
2.7711-2.82150.27961280.20511282X-RAY DIFFRACTION100
2.8215-2.87570.27091390.19861273X-RAY DIFFRACTION100
2.8757-2.93440.33071440.19871231X-RAY DIFFRACTION100
2.9344-2.99820.28651460.1781289X-RAY DIFFRACTION100
2.9982-3.0680.27821360.17391286X-RAY DIFFRACTION100
3.068-3.14470.27581500.16791245X-RAY DIFFRACTION100
3.1447-3.22970.2571160.1661238X-RAY DIFFRACTION100
3.2297-3.32470.24361540.15661263X-RAY DIFFRACTION100
3.3247-3.4320.26441310.15551263X-RAY DIFFRACTION100
3.432-3.55460.23211460.15591268X-RAY DIFFRACTION100
3.5546-3.69690.26121420.16041244X-RAY DIFFRACTION100
3.6969-3.86510.23051500.16591263X-RAY DIFFRACTION100
3.8651-4.06870.22061180.15231258X-RAY DIFFRACTION100
4.0687-4.32350.22891540.15881283X-RAY DIFFRACTION100
4.3235-4.65710.21460.16371238X-RAY DIFFRACTION100
4.6571-5.12520.22761390.17211243X-RAY DIFFRACTION100
5.1252-5.86570.26841450.20531248X-RAY DIFFRACTION100
5.8657-7.38580.26421340.20351285X-RAY DIFFRACTION100
7.3858-47.87640.19411270.16821258X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 49.9039 Å / Origin y: -129.3409 Å / Origin z: 118.9747 Å
111213212223313233
T0.2677 Å20.0096 Å20.0086 Å2-0.2684 Å2-0.0114 Å2--0.3633 Å2
L0.2616 °20.0266 °2-0.0287 °2-0.9263 °2-1.0944 °2--2.9892 °2
S-0.0188 Å °-0.077 Å °-0.0083 Å °-0.0168 Å °0.0724 Å °-0.06 Å °-0.0343 Å °-0.2047 Å °-0.0622 Å °
Refinement TLS groupSelection details: all

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