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- PDB-4yyz: 11B-HYDROXYSTEROID DEHYDROGENASE TYPE I IN COMPLEX WITH INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 4yyz
Title11B-HYDROXYSTEROID DEHYDROGENASE TYPE I IN COMPLEX WITH INHIBITOR
ComponentsCorticosteroid 11-beta-dehydrogenase isozyme 1
KeywordsOXIDOREDUCTASE / DEHYDROGENASE INHIBITOR / BHSD
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4JX / 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
AuthorsBranden, G. / Boden, C. / Ogg, D.
CitationJournal: Medchemcomm / Year: 2016
Title: Design of pyrozolo-pyrimidines as 11beta-HSD1 inhibitors through optimisation of molecular electrostatic potential.
Authors: Robb, G.R. / Boyd, S. / Davies, C.D. / Dossiter, A.G. / Goldberg, F.W. / Kemmitt, P.D. / Scott, J.S. / Swales, J.G.
History
DepositionMar 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9366
Polymers56,7682
Non-polymers2,1684
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-59 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.788, 107.788, 136.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 28383.988 Da / Num. of mol.: 2 / Fragment: UNP residues 26-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1, HSD11, HSD11L
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-4JX / N-[(1R,2s,3S,5s,7s)-5-hydroxytricyclo[3.3.1.1~3,7~]dec-2-yl]-5,7-dimethylpyrazolo[1,5-a]pyrimidine-3-carboxamide


Mass: 340.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N4O2

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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: 4.03 Å3/Da / Density % sol: 69.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20mM HEPES, 100mM NaCl, 2mM TCEP, 10uM NADP / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2010
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 3.15→46.67 Å / Num. obs: 15792 / % possible obs: 97.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 109.67 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 6.3
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
BUSTER2.11.6refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→19.75 Å / Cor.coef. Fo:Fc: 0.9149 / Cor.coef. Fo:Fc free: 0.8787 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.441
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 751 5 %RANDOM
Rwork0.2181 ---
obs0.2204 15023 97.1 %-
Displacement parametersBiso mean: 139.34 Å2
Baniso -1Baniso -2Baniso -3
1--15.1642 Å20 Å20 Å2
2---15.1642 Å20 Å2
3---30.3284 Å2
Refine analyzeLuzzati coordinate error obs: 0.416 Å
Refinement stepCycle: LAST / Resolution: 3.2→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 146 0 4106
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014291HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.245914HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1519SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes700HARMONIC5
X-RAY DIFFRACTIONt_it4291HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion22.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion560SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5362SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3495 162 5.92 %
Rwork0.3173 2575 -
all0.3193 2737 -
obs--99.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
14.5455-1.12810.34893.0116-0.76599.13420.2978-0.2029-0.387-0.22140.1132-0.2960.59762.2305-0.411-0.5903-0.1997-0.07020.6758-0.1745-0.2358Chain A51.3505-43.784520.335
23.17080.94530.61292.9701-0.52826.88160.20630.25740.6738-0.0980.33740.3554-1.92240.0641-0.54370.1788-0.45270.2348-0.15610.0982-0.198Chain B33.6269-21.44599.4294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ B|* }
2X-RAY DIFFRACTION2{ B|* }

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