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- PDB-3d5q: Crystal Structure of 11b-HSD1 in Complex with Triazole Inhibitor -

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Basic information

Entry
Database: PDB / ID: 3d5q
TitleCrystal Structure of 11b-HSD1 in Complex with Triazole Inhibitor
ComponentsCorticosteroid 11-beta-dehydrogenase isozyme 1
KeywordsOXIDOREDUCTASE / 11beta / hydroxysteroid / dehydrogenase / Endoplasmic reticulum / Glycoprotein / Lipid metabolism / Membrane / Microsome / NADP / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-T30 / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.55 Å
AuthorsWang, Z. / Liu, J. / Sudom, A. / Walker, N.P.C.
CitationJournal: Bioorg.Med.Chem. / Year: 2008
Title: Distinctive molecular inhibition mechanisms for selective inhibitors of human 11beta-hydroxysteroid dehydrogenase type 1.
Authors: Tu, H. / Powers, J.P. / Liu, J. / Ursu, S. / Sudom, A. / Yan, X. / Xu, H. / Meininger, D. / Degraffenreid, M. / He, X. / Jaen, J.C. / Sun, D. / Labelle, M. / Yamamoto, H. / Shan, B. / Walker, N.P. / Wang, Z.
History
DepositionMay 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Feb 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)124,51112
Polymers119,9154
Non-polymers4,5958
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16210 Å2
ΔGint-129 kcal/mol
Surface area40220 Å2
MethodPISA
2
A: Corticosteroid 11-beta-dehydrogenase isozyme 1
B: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2556
Polymers59,9582
Non-polymers2,2984
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-58 kcal/mol
Surface area21230 Å2
MethodPISA
3
C: Corticosteroid 11-beta-dehydrogenase isozyme 1
D: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2556
Polymers59,9582
Non-polymers2,2984
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-49 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.675, 153.319, 73.601
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29978.857 Da / Num. of mol.: 4 / 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-T30 / 3-[1-(4-fluorophenyl)cyclopropyl]-4-(1-methylethyl)-5-[4-(trifluoromethoxy)phenyl]-4H-1,2,4-triazole


Mass: 405.389 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H19F4N3O

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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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.4
Details: 19% 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 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2005 / Details: 3X3 CCD ARRAY
RadiationMonochromator: DOUBLE-CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.55→76.696 Å / Num. all: 40889 / Num. obs: 40780 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 69.4 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 10.2
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.2.5data scaling
REFMAC5.4.0069refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementResolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.598 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.736 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2012 4.9 %RANDOM
Rwork0.23 ---
obs0.232 40744 99.7 %-
all-38732 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.03 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å2-2.81 Å2
2---1.85 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8003 0 308 0 8311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228473
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.52.01211500
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61251031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48324.038312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.934151490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9041537
X-RAY DIFFRACTIONr_chiral_restr0.0830.21347
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026042
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_it0.5641.55148
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05528286
X-RAY DIFFRACTIONr_scbond_it1.23433325
X-RAY DIFFRACTIONr_scangle_it2.134.53202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 141 -
Rwork0.291 2851 -
obs--100 %

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