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- PDB-2ilt: Human 11-beta-Hydroxysteroid Dehydrogenase (HSD1) with NADP and A... -

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Basic information

Entry
Database: PDB / ID: 2ilt
TitleHuman 11-beta-Hydroxysteroid Dehydrogenase (HSD1) with NADP and Adamantane Sulfone Inhibitor
ComponentsCorticosteroid 11-beta-dehydrogenase isozyme 1
KeywordsOXIDOREDUCTASE / HSD1 / NADP / inhibitor
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 / NICKEL (II) ION / Chem-NN1 / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLongenecker, K.L. / Sorensen, B. / Judge, R. / Qin, W. / Link, J.T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Adamantane sulfone and sulfonamide 11-beta-HSD1 Inhibitors.
Authors: Sorensen, B. / Winn, M. / Rohde, J. / Shuai, Q. / Wang, J. / Fung, S. / Monzon, K. / Chiou, W. / Stolarik, D. / Imade, H. / Pan, L. / Deng, X. / Chovan, L. / Longenecker, K. / Judge, R. / ...Authors: Sorensen, B. / Winn, M. / Rohde, J. / Shuai, Q. / Wang, J. / Fung, S. / Monzon, K. / Chiou, W. / Stolarik, D. / Imade, H. / Pan, L. / Deng, X. / Chovan, L. / Longenecker, K. / Judge, R. / Qin, W. / Brune, M. / Camp, H. / Frevert, E.U. / Jacobson, P. / Link, J.T.
History
DepositionOct 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7235
Polymers30,4181
Non-polymers1,3054
Water3,117173
1
A: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules

A: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,44610
Polymers60,8362
Non-polymers2,6108
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area9110 Å2
ΔGint-61 kcal/mol
Surface area24620 Å2
MethodPISA
2
A: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)380,67460
Polymers365,01712
Non-polymers15,65748
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area79560 Å2
ΔGint-517 kcal/mol
Surface area123740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.871, 123.871, 123.871
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-801-

NI

21A-802-

NI

31A-903-

HOH

41A-990-

HOH

51A-991-

HOH

61A-1012-

HOH

71A-1030-

HOH

DetailsThe monomer of the asymmetric unit constitutes half of a biologically relevant dimer formed by the symmetry operator 1-X, Y, 1-Z

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Components

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


Mass: 30418.113 Da / Num. of mol.: 1 / Fragment: dehydrogenase domain (residues 23-284)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1
References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-NN1 / 2-(2-CHLORO-4-FLUOROPHENOXY)-2-METHYL-N-[(1R,2S,3S,5S,7S)-5-(METHYLSULFONYL)-2-ADAMANTYL]PROPANAMIDE


Mass: 443.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27ClFNO4S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→87.71 Å / Num. obs: 14223 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.067 / Χ2: 1.1 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.388.70.4714130.861100
2.38-2.489.70.39414200.8721100
2.48-2.5910.10.30613800.9341100
2.59-2.7310.50.26314231.0411100
2.73-2.9110.17814061.0711100
2.9-3.1211.20.12714011.1391100
3.12-3.4411.20.08514251.3061100
3.44-3.9311.20.05414221.4771100
3.93-4.9511.10.03714541.3291100
4.95-5010.70.02314790.848199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→87.71 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.826 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.378 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 713 5 %RANDOM
Rwork0.209 ---
obs0.212 14220 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.773 Å2
Refinement stepCycle: LAST / Resolution: 2.3→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 79 173 2382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212254
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9923063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0645274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74824.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13615389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.878159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021640
X-RAY DIFFRACTIONr_nbd_refined0.1990.21084
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.224
X-RAY DIFFRACTIONr_mcbond_it0.6191.51413
X-RAY DIFFRACTIONr_mcangle_it1.04422192
X-RAY DIFFRACTIONr_scbond_it1.4423961
X-RAY DIFFRACTIONr_scangle_it2.2394.5871
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 56 -
Rwork0.21 983 -
obs-1039 100 %

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