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- PDB-3hfg: Crystal Structure of Human 11-beta-hydroxysteroid-dehydrogenase B... -

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Basic information

Entry
Database: PDB / ID: 3hfg
TitleCrystal Structure of Human 11-beta-hydroxysteroid-dehydrogenase Bound to an Sulfonyl-piperazine Inhibitor
ComponentsCorticosteroid 11-beta-dehydrogenase isozyme 1
KeywordsOXIDOREDUCTASE / HSD1 / NADP / inhibitor / Endoplasmic reticulum / Glycoprotein / Lipid metabolism / Membrane / Polymorphism / Signal-anchor / Steroid metabolism / Transmembrane
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-17R / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Rigid Body Refinement / Resolution: 2.3 Å
AuthorsBard, J. / Svenson, K.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Efficacious 11beta-hydroxysteroid dehydrogenase type I inhibitors in the diet-induced obesity mouse model.
Authors: Wan, Z.K. / Chenail, E. / Xiang, J. / Li, H.Q. / Ipek, M. / Bard, J. / Svenson, K. / Mansour, T.S. / Xu, X. / Tian, X. / Suri, V. / Hahm, S. / Xing, Y. / Johnson, C.E. / Li, X. / Qadri, A. / ...Authors: Wan, Z.K. / Chenail, E. / Xiang, J. / Li, H.Q. / Ipek, M. / Bard, J. / Svenson, K. / Mansour, T.S. / Xu, X. / Tian, X. / Suri, V. / Hahm, S. / Xing, Y. / Johnson, C.E. / Li, X. / Qadri, A. / Panza, D. / Perreault, M. / Tobin, J.F. / Saiah, E.
History
DepositionMay 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 13, 2021Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_unobs_or_zero_occ_atoms / 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 / _diffrn_source.type / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)132,19912
Polymers127,3484
Non-polymers4,8518
Water2,558142
1
A: Corticosteroid 11-beta-dehydrogenase isozyme 1
B: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0996
Polymers63,6742
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-53 kcal/mol
Surface area19790 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)66,0996
Polymers63,6742
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-54 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.438, 152.670, 74.203
Angle α, β, γ (deg.)90.000, 92.410, 90.000
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 residue 24-292, Lumenal / Mutation: C272S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1, HSD11, HSD11L / Production host: Escherichia coli (E. coli)
References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase
#2: Chemical
ChemComp-17R / (2R)-4-[4-fluoro-2-(trifluoromethyl)phenyl]-2-methyl-1-{[3-(1H-1,2,4-triazol-1-yl)phenyl]sulfonyl}piperazine / (R)-1-(3-(1H-1,2,4-triazol-1-yl)phenylsulfonyl)-4-(4-fluoro-2-(trifluoromethyl)phenyl)-2-methylpiperazine


Mass: 469.456 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H19F4N5O2S
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 16.4 % PEG 3350, 100 mM MES pH 7.1, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Mar 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 54010 / % possible obs: 98.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.091 / Χ2: 1.146 / Net I/σ(I): 10.318
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.382.40.92853440.97997.1
2.38-2.482.40.76753201.02297.4
2.48-2.592.40.5853611.0697.7
2.59-2.732.50.43153921.06298.3
2.73-2.92.50.30653931.16598.4
2.9-3.122.60.21554561.28498.5
3.12-3.442.70.13953661.3398.5
3.44-3.932.70.0954471.48298.5
3.93-4.952.90.06454431.1998.7
4.95-503.10.04554880.86798.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
PHENIX1.4_6refinement
RefinementMethod to determine structure: Rigid Body Refinement / Resolution: 2.3→28.233 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 1.89 / σ(F): 0.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.285 2330 5.05 %
Rwork0.231 --
obs0.234 46174 83.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.548 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso max: 106.2 Å2 / Biso mean: 55.475 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-18.817 Å2-0 Å2-8.099 Å2
2---7.158 Å2-0 Å2
3----11.66 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7755 0 320 142 8217

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