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- PDB-3oq1: Crystal Structure of 11beta-Hydroxysteroid Dehydrogenase-1 (11b-H... -

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Basic information

Entry
Database: PDB / ID: 3oq1
TitleCrystal Structure of 11beta-Hydroxysteroid Dehydrogenase-1 (11b-HSD1) in Complex with Diarylsulfone Inhibitor
ComponentsCorticosteroid 11-beta-dehydrogenase isozyme 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / oxidoreductase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development ...11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development / NADP binding / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein homodimerization activity / membrane
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3OQ / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsWang, Z. / Sudom, A. / Walker, N.P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: The synthesis and SAR of novel diarylsulfone 11beta-HSD1 inhibitors
Authors: Yan, X. / Wang, Z. / Sudom, A. / Cardozo, M. / DeGraffenreid, M. / Di, Y. / Fan, P. / He, X. / Jaen, J.C. / Labelle, M. / Liu, J. / Ma, J. / McMinn, D. / Miao, S. / Sun, D. / Tang, L. / Tu, ...Authors: Yan, X. / Wang, Z. / Sudom, A. / Cardozo, M. / DeGraffenreid, M. / Di, Y. / Fan, P. / He, X. / Jaen, J.C. / Labelle, M. / Liu, J. / Ma, J. / McMinn, D. / Miao, S. / Sun, D. / Tang, L. / Tu, H. / Ursu, S. / Walker, N. / Ye, Q. / Powers, J.P.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Non-polymer description
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Corticosteroid 11-beta-dehydrogenase isozyme 1
B: Corticosteroid 11-beta-dehydrogenase isozyme 1
C: Corticosteroid 11-beta-dehydrogenase isozyme 1
D: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,92712
Polymers127,3484
Non-polymers4,5798
Water55831
1
A: Corticosteroid 11-beta-dehydrogenase isozyme 1
B: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9636
Polymers63,6742
Non-polymers2,2904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-62 kcal/mol
Surface area21200 Å2
MethodPISA
2
C: Corticosteroid 11-beta-dehydrogenase isozyme 1
D: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9636
Polymers63,6742
Non-polymers2,2904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-52 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.303, 153.398, 73.593
Angle α, β, γ (deg.)90.00, 92.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Corticosteroid 11-beta-dehydrogenase isozyme 1 / 11-beta-hydroxysteroid dehydrogenase 1 / 11-beta-HSD1 / 11-DH


Mass: 31836.875 Da / Num. of mol.: 4 / Fragment: UNP residues 24-292 / Mutation: C272S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1, HSD11, HSD11L / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): DH10a
References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-3OQ / 3-(2-fluoroethyl)-4-({4-[(2S)-1,1,1-trifluoro-2-hydroxypropan-2-yl]phenyl}sulfonyl)benzonitrile


Mass: 401.375 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H15F4NO3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.4
Details: 16% PEG 3350, 0.1 M MES 6.4, vapor diffusion, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorType: ADSCQ315 / Detector: CCD / Date: Jun 11, 2005 / Details: 3X3 CCD ARRAY
RadiationMonochromator: DOUBLE-CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→38.042 Å / Num. all: 38303 / Num. obs: 36893 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.6-2.743.60.4061.70.406195
2.74-2.913.60.2642.60.264194.2
2.91-3.113.50.1873.60.187193.7
3.11-3.363.50.1225.50.122194.8
3.36-3.683.40.08970.089198
3.68-4.113.40.06990.069199.4
4.11-4.753.60.05710.50.057199.9
4.75-5.813.70.0512.10.05199.9
5.81-8.223.60.03815.70.038199.8
8.22-66.3723.10.03120.70.031188.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.94 Å38.03 Å
Translation2.94 Å38.03 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.5data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→38 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.875 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.645 / SU ML: 0.333 / SU R Cruickshank DPI: 1.8644 / Cross valid method: THROUGHOUT / ESU R: 1.603 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30761 1843 5 %RANDOM
Rwork0.2195 ---
obs0.22395 35016 96.16 %-
all-38303 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.466 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å2-2.24 Å2
2---1.2 Å20 Å2
3----2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8124 0 300 31 8455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228601
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7182.00611678
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9551058
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17723.994318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.153151502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4961537
X-RAY DIFFRACTIONr_chiral_restr0.1070.21362
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026152
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7541.55248
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4128442
X-RAY DIFFRACTIONr_scbond_it1.81333353
X-RAY DIFFRACTIONr_scangle_it3.0194.53234
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 142 -
Rwork0.352 2556 -
obs--94.93 %

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