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- PDB-9w6v: Crystal structure of 11betaHSD1 in complex with compound 1 -

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Basic information

Entry
Database: PDB / ID: 9w6v
TitleCrystal structure of 11betaHSD1 in complex with compound 1
Components11-beta-hydroxysteroid dehydrogenase 1
KeywordsOXIDOREDUCTASE / Lipid metabolism
Function / homology
Function and homology information


cortisol dehydrogenase (NADP+) activity / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / 11beta-hydroxysteroid dehydrogenase / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development ...cortisol dehydrogenase (NADP+) activity / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / 11beta-hydroxysteroid dehydrogenase / 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 domain superfamily
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTakahashi, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem. / Year: 2025
Title: Structure-based design, synthesis, and evaluation of tetrahydrotriazolothiazepine derivatives as novel 11 beta-hydroxysteroid dehydrogenase type 1 inhibitors
Authors: Numata, Y. / Hasegawa, T. / Mori, M. / Shinozuka, T. / Yamamoto, Y. / Honzumi, M. / Kanayama, C. / Aoyagi, A. / Abe, M. / Ofune, Y. / Suzuki, K. / Imamura, Y. / Yahara, C. / Obuchi, W. / ...Authors: Numata, Y. / Hasegawa, T. / Mori, M. / Shinozuka, T. / Yamamoto, Y. / Honzumi, M. / Kanayama, C. / Aoyagi, A. / Abe, M. / Ofune, Y. / Suzuki, K. / Imamura, Y. / Yahara, C. / Obuchi, W. / Moritomo, A. / Takahashi, M.
History
DepositionAug 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
E: 11-beta-hydroxysteroid dehydrogenase 1
F: 11-beta-hydroxysteroid dehydrogenase 1
G: 11-beta-hydroxysteroid dehydrogenase 1
H: 11-beta-hydroxysteroid dehydrogenase 1
I: 11-beta-hydroxysteroid dehydrogenase 1
J: 11-beta-hydroxysteroid dehydrogenase 1
K: 11-beta-hydroxysteroid dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,91833
Polymers293,75511
Non-polymers11,16322
Water00
1
A: 11-beta-hydroxysteroid dehydrogenase 1
B: 11-beta-hydroxysteroid dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4406
Polymers53,4102
Non-polymers2,0304
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-38 kcal/mol
Surface area20210 Å2
MethodPISA
2
C: 11-beta-hydroxysteroid dehydrogenase 1
D: 11-beta-hydroxysteroid dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4406
Polymers53,4102
Non-polymers2,0304
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-37 kcal/mol
Surface area19550 Å2
MethodPISA
3
E: 11-beta-hydroxysteroid dehydrogenase 1
F: 11-beta-hydroxysteroid dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4406
Polymers53,4102
Non-polymers2,0304
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-35 kcal/mol
Surface area19740 Å2
MethodPISA
4
G: 11-beta-hydroxysteroid dehydrogenase 1
H: 11-beta-hydroxysteroid dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4406
Polymers53,4102
Non-polymers2,0304
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-38 kcal/mol
Surface area20100 Å2
MethodPISA
5
I: 11-beta-hydroxysteroid dehydrogenase 1
J: 11-beta-hydroxysteroid dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4406
Polymers53,4102
Non-polymers2,0304
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-38 kcal/mol
Surface area20280 Å2
MethodPISA
6
K: 11-beta-hydroxysteroid dehydrogenase 1
hetero molecules

K: 11-beta-hydroxysteroid dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4406
Polymers53,4102
Non-polymers2,0304
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_7511-x+2,y,-z+61
Buried area5500 Å2
ΔGint-38 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)308.090, 99.370, 136.245
Angle α, β, γ (deg.)90.00, 104.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
11-beta-hydroxysteroid dehydrogenase 1 / 11-DH / 11-beta-HSD1 / 7-oxosteroid reductase / Corticosteroid 11-beta-dehydrogenase isozyme 1 / ...11-DH / 11-beta-HSD1 / 7-oxosteroid reductase / Corticosteroid 11-beta-dehydrogenase isozyme 1 / Short chain dehydrogenase/reductase family 26C member 1


Mass: 26705.031 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1, HSD11, HSD11L, SDR26C1 / Production host: Escherichia coli B (bacteria)
References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase, 7beta-hydroxysteroid dehydrogenase (NADP+)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-A1MBC / 3-(1-adamantyl)-6,7,8,9-tetrahydro-5~{H}-[1,2,4]triazolo[4,3-a]azepine / MERCK-544 / Compound 544


Mass: 271.401 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C17H25N3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 3.44 Å3/Da / Density % sol: 64.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG8000, 8% ethylene glycol and 0.1 M HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 65803 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rsym value: 0.071 / Net I/σ(I): 14.7
Reflection shellResolution: 3.2→3.31 Å / Num. unique obs: 6278 / Rsym value: 0.274 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XU9

1xu9


Resolution: 3.2→49.69 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 6521 9.92 %
Rwork0.1868 --
obs0.194 65754 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19994 0 748 0 20742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121158
X-RAY DIFFRACTIONf_angle_d1.27528712
X-RAY DIFFRACTIONf_dihedral_angle_d7.3353062
X-RAY DIFFRACTIONf_chiral_restr0.0613379
X-RAY DIFFRACTIONf_plane_restr0.0083462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.240.38191810.29511776X-RAY DIFFRACTION89
3.24-3.270.29732030.26261842X-RAY DIFFRACTION95
3.27-3.310.35812040.25782007X-RAY DIFFRACTION97
3.31-3.350.33012000.23271899X-RAY DIFFRACTION99
3.35-3.40.31822240.23041977X-RAY DIFFRACTION100
3.4-3.450.31822290.24022009X-RAY DIFFRACTION100
3.45-3.490.33172000.23721937X-RAY DIFFRACTION100
3.49-3.550.33082140.23831999X-RAY DIFFRACTION100
3.55-3.60.31432340.2261949X-RAY DIFFRACTION100
3.6-3.660.29332210.21051994X-RAY DIFFRACTION100
3.66-3.720.30721900.19931983X-RAY DIFFRACTION100
3.72-3.790.27212230.19631973X-RAY DIFFRACTION100
3.79-3.870.25992050.2031985X-RAY DIFFRACTION100
3.87-3.940.3071980.20562009X-RAY DIFFRACTION100
3.94-4.030.28692510.18741941X-RAY DIFFRACTION100
4.03-4.120.24352310.18712011X-RAY DIFFRACTION100
4.12-4.230.24922400.18111922X-RAY DIFFRACTION100
4.23-4.340.26552060.17782008X-RAY DIFFRACTION100
4.34-4.470.24392440.15791948X-RAY DIFFRACTION100
4.47-4.610.23312040.15171976X-RAY DIFFRACTION100
4.61-4.780.23582120.15822033X-RAY DIFFRACTION100
4.78-4.970.26011910.16642022X-RAY DIFFRACTION100
4.97-5.190.23732390.17091965X-RAY DIFFRACTION100
5.19-5.470.23882480.17921980X-RAY DIFFRACTION100
5.47-5.810.2362220.17761988X-RAY DIFFRACTION100
5.81-6.260.27862060.18671998X-RAY DIFFRACTION100
6.26-6.890.21582310.16762003X-RAY DIFFRACTION100
6.89-7.880.21172190.15152009X-RAY DIFFRACTION100
7.88-9.910.18422260.13382033X-RAY DIFFRACTION100
9.91-49.690.21642250.18742057X-RAY DIFFRACTION99

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