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- PDB-4gjd: Crystal structure of renin in complex with NVP-BGQ311 (compound 12) -

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Basic information

Entry
Database: PDB / ID: 4gjd
TitleCrystal structure of renin in complex with NVP-BGQ311 (compound 12)
ComponentsRenin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / renin inhibitor / fragment based screening / 3 / 5-disubstituted piperidines / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins ...renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / amyloid-beta metabolic process / cell maturation / response to cAMP / insulin-like growth factor receptor binding / hormone-mediated signaling pathway / 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 / FOURIER SYNTHESIS / Resolution: 2.65 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

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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)76,0076
Polymers74,5342
Non-polymers1,4734
Water5,405300
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1624
Polymers37,2671
Non-polymers8953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8452
Polymers37,2671
Non-polymers5781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.917, 141.917, 141.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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-0N0 / (3S,5R)-N-{[9-(4-methoxybutyl)-9H-xanthen-9-yl]methyl}-5-{[(4-methylphenyl)sulfonyl]amino}piperidine-3-carboxamide


Mass: 577.734 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H39N3O5S
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 3.2 Å3/Da / Density % sol: 61.51 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95577 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 11, 2005
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95577 Å / Relative weight: 1
ReflectionResolution: 2.65→47.3 Å / Num. obs: 27679 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Redundancy: 4 % / Biso Wilson estimate: 67.37 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.4
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

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

2v0z


Resolution: 2.65→44.86 Å / Cor.coef. Fo:Fc: 0.9409 / Cor.coef. Fo:Fc free: 0.9114 / SU R Cruickshank DPI: 0.492 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.536 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.269 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 2772 10.05 %RANDOM
Rwork0.1799 ---
obs0.1844 27590 98.79 %-
Displacement parametersBiso mean: 50.07 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.289 Å
Refinement stepCycle: LAST / Resolution: 2.65→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5182 0 101 300 5583
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015415HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.227357HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1802SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes112HARMONIC2
X-RAY DIFFRACTIONt_gen_planes789HARMONIC5
X-RAY DIFFRACTIONt_it5415HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion17.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion716SEMIHARMONIC5
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_contact6103SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.75 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2852 290 10.39 %
Rwork0.2185 2502 -
all0.2253 2792 -
obs-2792 98.79 %

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