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- PDB-3oqf: Crystal Structure Analysis of Renin-indole-piperazine inhibitor c... -

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Basic information

Entry
Database: PDB / ID: 3oqf
TitleCrystal Structure Analysis of Renin-indole-piperazine 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 / 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 / FOURIER SYNTHESIS / Resolution: 2.78 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 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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

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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)75,7676
Polymers74,5342
Non-polymers1,2334
Water3,513195
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8843
Polymers37,2671
Non-polymers6172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8843
Polymers37,2671
Non-polymers6172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.220, 143.220, 143.220
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-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-S51 / 2-benzyl-1-phenyl-3-(piperazin-1-ylcarbonyl)-1H-indole / (2-Benzyl-1-phenyl-1H-indol-3-yl)-piperazin-1-yl-methanone


Mass: 395.496 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H25N3O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 3.31 Å3/Da / Density % sol: 62.88 %
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 / 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: 2.78→71.61 Å / Num. all: 24822 / Num. obs: 24795 / Redundancy: 4.8 % / Rmerge(I) obs: 0.138
Reflection shellResolution: 2.78→2.93 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3587 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.9.5refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
BUSTER2.9.5refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.78→71.61 Å / Cor.coef. Fo:Fc: 0.9304 / Cor.coef. Fo:Fc free: 0.9133 / Occupancy max: 1 / Occupancy min: 1 / 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
Rfree0.2013 1224 4.94 %RANDOM
Rwork0.1798 ---
obs0.1809 24795 99.45 %-
Displacement parametersBiso max: 151.1 Å2 / Biso mean: 51.1141 Å2 / Biso min: 22.43 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.78→71.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 88 195 5479
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d18002
X-RAY DIFFRACTIONt_trig_c_planes1182
X-RAY DIFFRACTIONt_gen_planes7985
X-RAY DIFFRACTIONt_it543020
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_contact60234
X-RAY DIFFRACTIONt_bond_d543020.007
X-RAY DIFFRACTIONt_angle_deg737221.05
X-RAY DIFFRACTIONt_omega_torsion4.14
X-RAY DIFFRACTIONt_other_torsion18.09
LS refinement shellResolution: 2.78→2.9 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2568 142 4.87 %
Rwork0.1989 2775 -
all0.2016 2917 -
obs--99.45 %
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)
11.46520.72140.67492.53550.60264.25660.04040.045-0.30940.07040.1263-0.31320.17660.1624-0.1667-0.05160.0060.0238-0.1029-0.00240.0699-12.2853-37.666-1.3458
21.04840.20870.342.34780.40961.92920.0433-0.10540.03430.14010.0206-0.0250.01320.0134-0.06390.03550.01830.02410.02770.0030.0035-12.1027-16.129110.893
31.6244-0.10810.18381.8968-1.42753.3634-0.03260.0911-0.0282-0.09760.06650.18350.0889-0.1771-0.0339-0.0331-0.01840.0536-0.0289-0.00670.0322-43.5607-47.5586-13.5858
43.3825-0.5505-0.1473.4007-1.0022.9391-0.0410.2986-0.3925-0.11730.0988-0.28220.42520.2838-0.05780.03360.10080.0783-0.0472-0.05760.0879-23.0023-61.673-12.716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|-2 - A|11 A|146 - A|160 A|160 - A|326 }A-2 - 11
2X-RAY DIFFRACTION1{ A|-2 - A|11 A|146 - A|160 A|160 - A|326 }A146 - 160
3X-RAY DIFFRACTION1{ A|-2 - A|11 A|146 - A|160 A|160 - A|326 }A160 - 326
4X-RAY DIFFRACTION2{ A|12 - A|142 }A12 - 142
5X-RAY DIFFRACTION3{ B|-2 - B|11 B|146 - B|160 B|160 - B|326 }B-2 - 11
6X-RAY DIFFRACTION3{ B|-2 - B|11 B|146 - B|160 B|160 - B|326 }B146 - 160
7X-RAY DIFFRACTION3{ B|-2 - B|11 B|146 - B|160 B|160 - B|326 }B160 - 326
8X-RAY DIFFRACTION4{ B|12 - B|142 }B12 - 142

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