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- PDB-4gj9: Crystal structure of renin in complex with GP055321 (compound 4) -

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Basic information

Entry
Database: PDB / ID: 4gj9
TitleCrystal structure of renin in complex with GP055321 (compound 4)
ComponentsRenin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / renin inhibitor / fragment based screening / 3 / 5-disubstituted piperidines / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / response to immobilization stress / regulation of MAPK cascade / amyloid-beta metabolic process / response to cAMP ...renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / response to immobilization stress / regulation of MAPK cascade / amyloid-beta metabolic process / response to cAMP / Metabolism of Angiotensinogen to Angiotensins / cell maturation / angiotensin maturation / hormone-mediated signaling pathway / insulin-like growth factor receptor binding / kidney development / regulation of blood pressure / male gonad development / cellular response to xenobiotic stimulus / apical part of cell / peptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsOstermann, N. / Zink, F. / Kroemer, M.
CitationJournal: J.Med.Chem. / Year: 2013
Title: A novel class of oral direct Renin inhibitors: highly potent 3,5-disubstituted piperidines bearing a tricyclic p3-p1 pharmacophore.
Authors: Ostermann, N. / Ruedisser, S. / Ehrhardt, C. / Breitenstein, W. / Marzinzik, A. / Jacoby, E. / Vangrevelinghe, E. / Ottl, J. / Klumpp, M. / Hartwieg, J.C. / Cumin, F. / Hassiepen, U. / ...Authors: Ostermann, N. / Ruedisser, S. / Ehrhardt, C. / Breitenstein, W. / Marzinzik, A. / Jacoby, E. / Vangrevelinghe, E. / Ottl, J. / Klumpp, M. / Hartwieg, J.C. / Cumin, F. / Hassiepen, U. / Trappe, J. / Sedrani, R. / Geisse, S. / Gerhartz, B. / Richert, P. / Francotte, E. / Wagner, T. / Kromer, M. / Kosaka, T. / Webb, R.L. / Rigel, D.F. / Maibaum, J. / Baeschlin, D.K.
History
DepositionAug 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Renin
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5616
Polymers74,5342
Non-polymers1,0274
Water4,990277
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7813
Polymers37,2671
Non-polymers5142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7813
Polymers37,2671
Non-polymers5142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.000, 108.750, 138.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Renin / Angiotensinogenase


Mass: 37267.008 Da / Num. of mol.: 2 / Fragment: UNP residues 67-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00797, renin
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-0M2 / (2R)-1-(3,8-dihydrodibenzo[b,f]pyrrolo[3,4-d]azepin-2(1H)-yl)propan-2-ol


Mass: 292.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: reservoir: 18-21% PEG4000, 0.4-0.6 M sodium chloride, 50 mM sodium citrate, pH 4-5, protein solution: 10-15 mg/mL protein, 25 mM sodium chloride, 12.5 mM Tris, pH 8, drop: 1 uL protein ...Details: reservoir: 18-21% PEG4000, 0.4-0.6 M sodium chloride, 50 mM sodium citrate, pH 4-5, protein solution: 10-15 mg/mL protein, 25 mM sodium chloride, 12.5 mM Tris, pH 8, drop: 1 uL protein solution + 1 uL reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 1, 2003
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→48.141 Å / Num. obs: 31698 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 52.7 / Biso Wilson estimate: 64.94 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 1.6 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MOLREPphasing
BUSTER2.11.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V0Z

2v0z


Resolution: 2.6→48.141 Å / Cor.coef. Fo:Fc: 0.9416 / Cor.coef. Fo:Fc free: 0.9167 / SU R Cruickshank DPI: 0.353 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.378 / SU Rfree Blow DPI: 0.246 / SU Rfree Cruickshank DPI: 0.245 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 3179 10.05 %RANDOM
Rwork0.1808 ---
obs0.1853 31631 99.31 %-
Displacement parametersBiso mean: 55.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.2289 Å20 Å20 Å2
2---0.9726 Å20 Å2
3---1.2015 Å2
Refine analyzeLuzzati coordinate error obs: 0.289 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5131 0 72 277 5480
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015331HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.217239HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1769SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes112HARMONIC2
X-RAY DIFFRACTIONt_gen_planes780HARMONIC5
X-RAY DIFFRACTIONt_it5331HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion18.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion711SEMIHARMONIC5
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_contact5949SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.264 244 8.69 %
Rwork0.2066 2564 -
all0.2116 2808 -
obs-2808 99.31 %

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