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- PDB-3vuc: Human renin in complex with compound 5 -

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Basic information

Entry
Database: PDB / ID: 3vuc
TitleHuman renin in complex with compound 5
ComponentsRenin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Aspartyl protease / RAS / hypertension / inhibitor / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTakahashi, M. / Matsui, Y. / Hanzawa, H.
CitationJournal: Acs Med.Chem.Lett. / Year: 2012
Title: Discovery of DS-8108b, a Novel Orally Bioavailable Renin Inhibitor.
Authors: Nakamura, Y. / Fujimoto, T. / Ogawa, Y. / Sugita, C. / Miyazaki, S. / Tamaki, K. / Takahashi, M. / Matsui, Y. / Nagayama, T. / Manabe, K. / Mizuno, M. / Masubuchi, N. / Chiba, K. / Nishi, T.
History
DepositionJun 26, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Dec 25, 2019Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag
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_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 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)76,0996
Polymers74,5342
Non-polymers1,5654
Water3,819212
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0493
Polymers37,2671
Non-polymers7822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0493
Polymers37,2671
Non-polymers7822
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)228,29618
Polymers223,6026
Non-polymers4,69412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_577z+1/2,-x+5/2,-y+21
crystal symmetry operation12_774-y+5/2,-z+2,x-1/21
Buried area15460 Å2
ΔGint-48 kcal/mol
Surface area73980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.289, 141.289, 141.289
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Plasmid: pcDNA3.1 / Cell line (production host): 293F / Production host: Homo sapiens (human) / 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.: 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-HHE / (2R,4S,5S)-5-amino-6-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-2-ethyl-4-hydroxy-N-[(1R,2S,3S,5S,7S)-5-hydroxytricyclo[3.3.1.1~3,7~]dec-2-yl]hexanamide


Mass: 561.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H45ClN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 3.15 Å3/Da / Density % sol: 61 % / Mosaicity: 0.387 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 5-12% PEG 3350, 0.6M NaCl, 0.1M citrate pH3.0-4.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 29254 / % possible obs: 99.9 % / Redundancy: 11 % / Rmerge(I) obs: 0.064 / Χ2: 1.171 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.6911.10.32828621.0241100
2.69-2.811.10.24328891.0021100
2.8-2.9311.10.17329131.0171100
2.93-3.0811.10.12529131.0381100
3.08-3.2811.20.09529111.0751100
3.28-3.53110.07229031.2391100
3.53-3.8811.10.05629041.2531100
3.88-4.45110.04629631.356199.9
4.45-5.6110.03829431.2641100
5.6-5010.50.03430531.446199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VSX

3vsx


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.6 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.604 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 2847 9.9 %RANDOM
Rwork0.1838 ---
obs0.1896 28763 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 111.4 Å2 / Biso mean: 49.0698 Å2 / Biso min: 10.5 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5225 0 106 212 5543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225466
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.9797435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.415675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58224.17223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49615869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4591520
X-RAY DIFFRACTIONr_chiral_restr0.1130.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214084
X-RAY DIFFRACTIONr_mcbond_it0.8711.53345
X-RAY DIFFRACTIONr_mcangle_it1.67525407
X-RAY DIFFRACTIONr_scbond_it2.55932121
X-RAY DIFFRACTIONr_scangle_it4.1314.52028
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 193 -
Rwork0.243 1880 -
all-2073 -
obs--98.71 %
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)Origin x (Å)Origin y (Å)Origin z (Å)
10.3253-0.31220.14311.0893-0.21040.4053-0.0091-0.00020.00940.02650.0074-0.0505-0.01370.06740.00170.0354-0.019-0.00260.1047-0.00490.0359188.1974195.34993.2548
21.8241-0.27370.13671.1448-0.60750.6103-0.0584-0.06150.05220.09470.08180.0023-0.1138-0.0423-0.02350.0823-0.02410.00930.0373-0.01120.0075173.7489214.740694.9983
31.47090.424-0.07170.83790.022.36330.1114-0.18410.09830.1992-0.03520.0298-0.3813-0.2316-0.07620.19210.03770.04210.0592-0.01310.0255166.1075236.583582.2326
42.09550.96980.35510.9051-0.1310.89650.00610.0683-0.0464-0.01460.1036-0.0161-0.0497-0.1287-0.10970.07890.02340.02210.03680.01520.0186162.3827223.9761.7416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 155
2X-RAY DIFFRACTION2A156 - 340
3X-RAY DIFFRACTION3B1 - 155
4X-RAY DIFFRACTION4B156 - 340

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