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- PDB-3g49: N-(Pyridin-2-yl) Arylsulfonamide Inhibitors of 11b-Hydroxysteroid... -

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Basic information

Entry
Database: PDB / ID: 3g49
TitleN-(Pyridin-2-yl) Arylsulfonamide Inhibitors of 11b-Hydroxysteroid Dehydrogenase Type 1: Discovery of PF-915275
Components11-beta-hydroxysteroid dehydrogenase 1
KeywordsOxidoreductase/Oxidoreductase inhibitor / 11beta-hydroxysteroid dehydrogenase / inhibited / Endoplasmic reticulum / Glycoprotein / Lipid metabolism / Membrane / NADP / Oxidoreductase / Signal-anchor / Steroid metabolism / Transmembrane / 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 / steroid metabolic process / lung development / NADP binding / endoplasmic reticulum membrane / protein homodimerization activity
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-3G4 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPauly, T.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: N-(Pyridin-2-yl) arylsulfonamide inhibitors of 11beta-hydroxysteroid dehydrogenase type 1: Discovery of PF-915275.
Authors: Siu, M. / Johnson, T.O. / Wang, Y. / Nair, S.K. / Taylor, W.D. / Cripps, S.J. / Matthews, J.J. / Edwards, M.P. / Pauly, T.A. / Ermolieff, J. / Castro, A. / Hosea, N.A. / LaPaglia, A. / Fanjul, A.N. / Vogel, J.E.
History
DepositionFeb 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 11-beta-hydroxysteroid dehydrogenase 1
B: 11-beta-hydroxysteroid dehydrogenase 1
C: 11-beta-hydroxysteroid dehydrogenase 1
D: 11-beta-hydroxysteroid dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,56710
Polymers121,8014
Non-polymers3,7656
Water3,027168
1
A: 11-beta-hydroxysteroid dehydrogenase 1
B: 11-beta-hydroxysteroid dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7835
Polymers60,9012
Non-polymers1,8833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-54 kcal/mol
Surface area20950 Å2
MethodPISA
2
C: 11-beta-hydroxysteroid dehydrogenase 1
D: 11-beta-hydroxysteroid dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7835
Polymers60,9012
Non-polymers1,8833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-52 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.207, 83.599, 179.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 30450.328 Da / Num. of mol.: 4 / Fragment: Lumenal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: HSD11B1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6QLL4, 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-3G4 / 2-(6-{[(3-chloro-2-methylphenyl)sulfonyl]amino}pyridin-2-yl)-N,N-diethylacetamide


Mass: 395.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22ClN3O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.4 Å3/Da / Density % sol: 48.85 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 7, 2003 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 38125 / % possible obs: 91.8 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CNSrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→41.27 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.566 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 1.028 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22518 1958 5.1 %RANDOM
Rwork0.18899 ---
obs0.19087 36124 91.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.664 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8068 0 244 168 8480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0228490
X-RAY DIFFRACTIONr_bond_other_d0.0040.027830
X-RAY DIFFRACTIONr_angle_refined_deg2.931.98411508
X-RAY DIFFRACTIONr_angle_other_deg1.2532.9918160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.02951048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1670.21306
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.029302
X-RAY DIFFRACTIONr_gen_planes_other0.010.021738
X-RAY DIFFRACTIONr_nbd_refined0.2660.22147
X-RAY DIFFRACTIONr_nbd_other0.2630.29401
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1050.24934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2318
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2021.55208
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.07228340
X-RAY DIFFRACTIONr_scbond_it3.50933282
X-RAY DIFFRACTIONr_scangle_it5.4554.53168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 86
Rwork0.202 1912

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