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- PDB-4ryc: RENIN IN COMPLEXED WITH 4-methoxy-3-(3-methoxypropoxy)-N-{[(3S,4S... -

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Basic information

Entry
Database: PDB / ID: 4ryc
TitleRENIN IN COMPLEXED WITH 4-methoxy-3-(3-methoxypropoxy)-N-{[(3S,4S)-4-{[(4-methylphenyl)sulfonyl]amino}pyrrolidin-3-yl]methyl}-N-(propan-2-yl)benzamide INHIBITOR
ComponentsRenin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / 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 / amyloid-beta metabolic process ...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 / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins / cell maturation / response to cAMP / hormone-mediated signaling pathway / kidney development / insulin-like growth factor receptor binding / 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: 2.45 Å
AuthorsOstermann, N.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: trans-(3S,4S)-Disubstituted pyrrolidines as inhibitors of the human aspartyl protease renin. Part I: Prime site exploration using an amino linker.
Authors: Lorthiois, E. / Cumin, F. / Ehrhardt, C. / Kosaka, T. / Sellner, H. / Ostermann, N. / Francotte, E. / Wagner, T. / Maibaum, J.
History
DepositionDec 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Jul 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 1.4Jun 30, 2021Group: Data collection / Structure summary / Category: chem_comp / diffrn_detector
Item: _chem_comp.pdbx_synonyms / _diffrn_detector.detector / _diffrn_detector.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Renin
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2188
Polymers74,5342
Non-polymers1,6846
Water3,999222
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1184
Polymers37,2671
Non-polymers8513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1004
Polymers37,2671
Non-polymers8333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Renin
B: Renin
hetero molecules

A: Renin
B: Renin
hetero molecules

A: Renin
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,65424
Polymers223,6026
Non-polymers5,05218
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area16210 Å2
ΔGint-99 kcal/mol
Surface area73300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.719, 141.719, 141.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Renin / Angiotensinogenase


Mass: 37267.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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

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Non-polymers , 4 types, 226 molecules

#3: Chemical ChemComp-3ZK / 4-methoxy-3-(3-methoxypropoxy)-N-{[(3S,4S)-4-{[(4-methylphenyl)sulfonyl]amino}pyrrolidin-3-yl]methyl}-N-(propan-2-yl)benzamide


Mass: 533.680 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H39N3O6S
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 3.18 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: HANGING DROP, VAPOR DIFFUSION, 20 DEG C, 1 UL PROTEIN + 1 UL RESERVOIR; PROTEIN SOLUTION: 31.7 MG/ML RENIN, 12.5 MM TRIS PH 8, 25 MM NACL; RESERVOIR SOLUTION: 21% PEG4000, 50 MM NACITRATE PH ...Details: HANGING DROP, VAPOR DIFFUSION, 20 DEG C, 1 UL PROTEIN + 1 UL RESERVOIR; PROTEIN SOLUTION: 31.7 MG/ML RENIN, 12.5 MM TRIS PH 8, 25 MM NACL; RESERVOIR SOLUTION: 21% PEG4000, 50 MM NACITRATE PH 4.5, 600 MM NACL; SOAKING: DROP PLUS 2.5 UL RESERVOIR SOLUTION PLUS 10 MM COMPOUND AND 10% DMSO FOR 30 MIN; CRYO: SOAKING SOLUTION PLUS 15% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97933 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.45→33.07 Å / Num. obs: 34123 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 62.06 Å2
Reflection shellResolution: 2.45→2.54 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→33.07 Å / Cor.coef. Fo:Fc: 0.9458 / Cor.coef. Fo:Fc free: 0.9248 / SU R Cruickshank DPI: 0.318 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 3409 10.02 %RANDOM
Rwork0.1905 ---
obs0.1943 34020 96.99 %-
Displacement parametersBiso mean: 51.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.303 Å
Refinement stepCycle: LAST / Resolution: 2.45→33.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 111 222 5503
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015409HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.197347HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1806SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes110HARMONIC2
X-RAY DIFFRACTIONt_gen_planes790HARMONIC5
X-RAY DIFFRACTIONt_it5409HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.72
X-RAY DIFFRACTIONt_other_torsion17.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion722SEMIHARMONIC5
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_contact6132SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.52 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2837 278 9.88 %
Rwork0.2266 2535 -
all0.232 2813 -
obs--96.99 %

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