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- PDB-4wrh: AKR1C3 complexed with breakdown product of N-(tert-butyl)-2-(2-ch... -

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Basic information

Entry
Database: PDB / ID: 4wrh
TitleAKR1C3 complexed with breakdown product of N-(tert-butyl)-2-(2-chloro-4-(((3-mercapto-5-methyl-4H-1,2,4-triazol-4-yl)amino)methyl)-6-methoxyphenoxy)acetamide
ComponentsAldo-keto reductase family 1 member C3
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / oxidoreductase / inhibitor / complex / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


prostaglandin-F synthase / testosterone 17beta-dehydrogenase (NADP+) / prostaglandin D2 11-ketoreductase activity / ketoreductase activity / prostaglandin F synthase activity / cellular response to prostaglandin stimulus / cellular response to corticosteroid stimulus / macromolecule metabolic process / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase ...prostaglandin-F synthase / testosterone 17beta-dehydrogenase (NADP+) / prostaglandin D2 11-ketoreductase activity / ketoreductase activity / prostaglandin F synthase activity / cellular response to prostaglandin stimulus / cellular response to corticosteroid stimulus / macromolecule metabolic process / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / negative regulation of retinoic acid biosynthetic process / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / Delta4-3-oxosteroid 5beta-reductase activity / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / farnesol catabolic process / geranylgeranyl reductase activity / 3alpha-hydroxysteroid 3-dehydrogenase / cellular response to jasmonic acid stimulus / regulation of testosterone biosynthetic process / : / androsterone dehydrogenase activity / testosterone biosynthetic process / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / RA biosynthesis pathway / testosterone dehydrogenase (NAD+) activity / cellular response to prostaglandin D stimulus / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / ketosteroid monooxygenase activity / regulation of retinoic acid receptor signaling pathway / retinal metabolic process / testosterone 17-beta-dehydrogenase (NADP+) activity / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / aldo-keto reductase (NADPH) activity / all-trans-retinol dehydrogenase (NAD+) activity / cyclooxygenase pathway / positive regulation of endothelial cell apoptotic process / prostaglandin H2 endoperoxidase reductase activity / all-trans-retinol dehydrogenase (NADP+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / retinal dehydrogenase activity / bile acid binding / aldose reductase (NADPH) activity / retinoid metabolic process / prostaglandin metabolic process / renal absorption / steroid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Retinoid metabolism and transport / keratinocyte differentiation / cellular response to starvation / cellular response to calcium ion / response to nutrient / male gonad development / positive regulation of reactive oxygen species metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 5-methyl-4H-1,2,4-triazole-3-thiol / Chem-YY2 / Aldo-keto reductase family 1 member C3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsSquire, C.J. / Flanagan, J.U. / Yosaatmadja, Y.
CitationJournal: To Be Published
Title: Breakdown product of N-(tert-butyl)-2-(2-chloro-4-(((3-mercapto-5-methyl-4H-1,2,4-triazol-4-yl)amino)methyl)-6-methoxyphenoxy)acetamide trapped in active site of AKR1C3
Authors: Yosaatmadja, Y. / Ko, R.-W. / Flanagan, J.U. / Squire, C.J.
History
DepositionOct 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _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: Aldo-keto reductase family 1 member C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2616
Polymers37,9771
Non-polymers1,2835
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.509, 63.503, 95.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aldo-keto reductase family 1 member C3 / 17-beta-hydroxysteroid dehydrogenase type 5 / 17-beta-HSD 5 / 3-alpha-HSD type II / brain / 3-alpha- ...17-beta-hydroxysteroid dehydrogenase type 5 / 17-beta-HSD 5 / 3-alpha-HSD type II / brain / 3-alpha-hydroxysteroid dehydrogenase type 2 / 3-alpha-HSD type 2 / Chlordecone reductase homolog HAKRb / Dihydrodiol dehydrogenase 3 / DD3 / Dihydrodiol dehydrogenase type I / HA1753 / Indanol dehydrogenase / Prostaglandin F synthase / PGFS / Testosterone 17-beta-dehydrogenase 5 / Trans-1 / 2-dihydrobenzene-1 / 2-diol dehydrogenase


Mass: 37977.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C3, DDH1, HSD17B5, KIAA0119, PGFS / Plasmid: pet22b / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: P42330, Oxidoreductases, 3alpha-hydroxysteroid 3-dehydrogenase, indanol dehydrogenase, prostaglandin-F synthase, 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+), testosterone ...References: UniProt: P42330, Oxidoreductases, 3alpha-hydroxysteroid 3-dehydrogenase, indanol dehydrogenase, prostaglandin-F synthase, 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+), testosterone 17beta-dehydrogenase (NADP+), trans-1,2-dihydrobenzene-1,2-diol dehydrogenase

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Non-polymers , 5 types, 209 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-YY2 / 2-[4-(aminomethyl)-2-chloro-6-methoxyphenoxy]-N-tert-butylacetamide


Mass: 300.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21ClN2O3
#4: Chemical ChemComp-YY1 / 5-methyl-4H-1,2,4-triazole-3-thiol


Mass: 115.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N3S
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 200 mM sodium acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.826534 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826534 Å / Relative weight: 1
ReflectionResolution: 1.6→95.57 Å / Num. obs: 45804 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.9 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementStarting model: PDB ENTRY 3UWE

3uwe


Resolution: 1.6→52.89 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.731 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18708 2306 5 %RANDOM
Rwork0.17049 ---
obs0.17133 43428 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.157 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.6→52.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 0 83 204 2774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192675
X-RAY DIFFRACTIONr_bond_other_d0.0020.022531
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9993642
X-RAY DIFFRACTIONr_angle_other_deg0.8273.0065824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68523.846117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9415446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2521517
X-RAY DIFFRACTIONr_chiral_restr0.0790.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212990
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02610
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4441.0591281
X-RAY DIFFRACTIONr_mcbond_other0.4441.0571280
X-RAY DIFFRACTIONr_mcangle_it0.7511.5851605
X-RAY DIFFRACTIONr_mcangle_other0.7511.5871606
X-RAY DIFFRACTIONr_scbond_it0.6521.1441394
X-RAY DIFFRACTIONr_scbond_other0.6511.1441394
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0291.6872034
X-RAY DIFFRACTIONr_long_range_B_refined3.7659.4773251
X-RAY DIFFRACTIONr_long_range_B_other3.7659.4833252
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.604→1.646 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 168 -
Rwork0.23 3124 -
obs--98.68 %
Refinement TLS params.Method: refined / Origin x: 6.1569 Å / Origin y: -4.9153 Å / Origin z: -10.8776 Å
111213212223313233
T0.0047 Å20.0021 Å2-0.0046 Å2-0.0038 Å20.0035 Å2--0.0231 Å2
L0.857 °20.0024 °2-0.1167 °2-0.5819 °2-0.4196 °2--1.558 °2
S0.0032 Å °0.0417 Å °0.1222 Å °-0.0231 Å °-0.0313 Å °0.0334 Å °-0.0524 Å °0.0051 Å °0.028 Å °

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