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- PDB-3oqk: Crystal Structure Analysis of Renin-indole-piperazin inhibitor co... -

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Basic information

Entry
Database: PDB / ID: 3oqk
TitleCrystal Structure Analysis of Renin-indole-piperazin inhibitor complexes
ComponentsRenin
KeywordsHYDROLASE / RENIN HUMAN / ASPARTYL PROTEASE / RENIN INHIBITION / HYPERTENSION
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 / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsBocskei, Z.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: Discovery and optimization of a new class of potent and non-chiral indole-3-carboxamide-based renin inhibitors.
Authors: Scheiper, B. / Matter, H. / Steinhagen, H. / Stilz, U. / Bocskei, Z. / Fleury, V. / McCort, G.
History
DepositionSep 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
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_leaving_atom_flag / _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

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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)75,8637
Polymers74,5342
Non-polymers1,3295
Water2,594144
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8863
Polymers37,2671
Non-polymers6192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9784
Polymers37,2671
Non-polymers7113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.387, 141.387, 141.387
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
Cell line (production host): HUMAN EMBRYONIC KIDNEY CELL (CRL-1573)
Production host: HOMO SAPIENS (human) / References: UniProt: P00797, renin
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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-S52 / 2-phenoxy-1-phenyl-3-(piperazin-1-ylcarbonyl)-1H-indole / (2-Phenoxy-1-phenyl-1H-indol-3-yl)-piperazin-1-yl-methanone


Mass: 397.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H23N3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.19 Å3/Da / Density % sol: 61.42 %
Crystal growTemperature: 298 K / pH: 4.5
Details: 0.05M CITRATE PH=4.5, 10-12% PEG3350, 0.6M NACL, 20 MG/ML RENIN, VAPOUR DIFFUSION, HANGING DROP, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 23, 2006 / Details: OSMIC BLUEMIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 21155 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.697 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
BUSTER2.9.5refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.9→49.99 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.895 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: POSITION OF WATER MOLECULES WERE TAKEN FROM A HIGHER RESOLUTION STRUCTURE (2.05 A). WATERS WERE REFINED AND RETAINED ONLY IF THE ISOTROPIC DISPLACEMENT PARAMETER REMAINED BELOW 80 A**2
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1081 5.12 %RANDOM
Rwork0.222 ---
obs0.224 21100 99.8 %-
Displacement parametersBiso mean: 78.66 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 94 144 5434
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00954252
X-RAY DIFFRACTIONt_angle_deg1.1473672
X-RAY DIFFRACTIONt_dihedral_angle_d17982
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1182
X-RAY DIFFRACTIONt_gen_planes7985
X-RAY DIFFRACTIONt_it542520
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.35
X-RAY DIFFRACTIONt_other_torsion17.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion7165
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_contact61654
LS refinement shellResolution: 2.9→3.04 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2658 148 5.36 %
Rwork0.2331 2611 -
all0.2349 2759 -
obs--99.8 %

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