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

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Basic information

Entry
Database: PDB / ID: 3oot
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 / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins ...renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins / cell maturation / response to cAMP / angiotensin maturation / insulin-like growth factor receptor binding / hormone-mediated signaling pathway / kidney development / regulation of blood pressure / male gonad development / apical part of cell / cellular response to xenobiotic stimulus / 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: 2.55 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
DepositionAug 31, 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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)75,8926
Polymers74,5342
Non-polymers1,3574
Water2,162120
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9463
Polymers37,2671
Non-polymers6792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9463
Polymers37,2671
Non-polymers6792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.554, 143.554, 143.554
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 / 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 / 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-SSR / 2-(3-fluoro-2-methylbenzyl)-4-methyl-1-phenyl-3-(piperazin-1-ylcarbonyl)-1H-indol-5-ol / [2-(3-Fluoro-2-methyl-benzyl)-5-hydroxy-4-methyl-1-phenyl-1H-indol-3-yl]-piperazin-1-yl-methanone


Mass: 457.539 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H28FN3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.34 Å3/Da / Density % sol: 63.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.05M CITRATE PH=4.5, 10-12% PEG3350, 0.6M NACL, 20 MG/ML RENIN, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 23, 2006 / Details: Osmic blue mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 31582 / % possible obs: 97.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.102 / Χ2: 1.128 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.55-2.641.90.64331520.99698.3
2.64-2.752.20.52931961.10599.9
2.75-2.872.30.39931801.19599.9
2.87-3.022.30.29431901.18399.7
3.02-3.212.30.22231951.15399.4
3.21-3.462.30.14531661.20698.9
3.46-3.812.30.09631571.24297.7
3.81-4.362.30.0731111.15296.2
4.36-5.492.20.05631341.0196.1
5.49-502.20.05931010.98591.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.9.5refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.55→33.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9275 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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
Rfree0.2203 1571 4.98 %RANDOM
Rwork0.1823 ---
obs0.1841 31544 97.5 %-
Displacement parametersBiso max: 144.74 Å2 / Biso mean: 54.0084 Å2 / Biso min: 25.05 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: LAST / Resolution: 2.55→33.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 96 120 5412
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d17962
X-RAY DIFFRACTIONt_trig_c_planes1182
X-RAY DIFFRACTIONt_gen_planes7985
X-RAY DIFFRACTIONt_it542820
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
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_contact58044
X-RAY DIFFRACTIONt_bond_d542820.009
X-RAY DIFFRACTIONt_angle_deg737821.23
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion20.84
LS refinement shellResolution: 2.55→2.63 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2898 137 4.94 %
Rwork0.2402 2639 -
all0.2426 2776 -
obs--97.5 %

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