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- PDB-2g20: Ketopiperazine-Based Renin Inhibitors: Optimization of the C Ring -

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Basic information

Entry
Database: PDB / ID: 2g20
TitleKetopiperazine-Based Renin Inhibitors: Optimization of the C Ring
ComponentsRenin
KeywordsHYDROLASE / PROTEIN-LIGAND COMPLEXES
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHolsworth, D.D. / Jalaiea, M. / Zhanga, E. / Mcconnella, P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Ketopiperazine-based renin inhibitors: optimization of the
Authors: Holsworth, D.D. / Cai, C. / Cheng, X.M. / Cody, W.L. / Downing, D.M. / Erasga, N. / Lee, C. / Powell, N.A. / Edmunds, J.J. / Stier, M. / Jalaie, M. / Zhang, E. / McConnell, P. / Ryan, M.J. / ...Authors: Holsworth, D.D. / Cai, C. / Cheng, X.M. / Cody, W.L. / Downing, D.M. / Erasga, N. / Lee, C. / Powell, N.A. / Edmunds, J.J. / Stier, M. / Jalaie, M. / Zhang, E. / McConnell, P. / Ryan, M.J. / Bryant, J. / Li, T. / Kasani, A. / Hall, E. / Subedi, R. / Rahim, M. / Maiti, S.
History
DepositionFeb 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)74,5464
Polymers73,1322
Non-polymers1,4142
Water1,856103
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2732
Polymers36,5661
Non-polymers7071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2732
Polymers36,5661
Non-polymers7071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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)223,63912
Polymers219,3976
Non-polymers4,2416
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area23290 Å2
ΔGint-69 kcal/mol
Surface area70390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.333, 141.333, 141.333
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: 36566.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Production host: Escherichia coli (E. coli) / References: UniProt: P00797, renin
#2: Chemical ChemComp-L1A / N-(MORPHOLIN-4-YLSULFONYL)-L-PHENYLALANYL-3-(2-AMINO-1,3-THIAZOL-4-YL)-N-{(1R,2R,3S)-1-[(1R)-CYCLOHEX-3-EN-1-YLMETHYL]-2,3-DIHYDROXY-5-METHYLHEXYL}-L-ALANINAMIDE


Mass: 706.916 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H50N6O7S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.22 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 36169 / % possible obs: 1 %
Reflection shellResolution: 2.4→50 Å / % possible all: 1

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.26 3617 RANDOM
Rwork0.21 --
obs0.21 36169 -
Displacement parametersBiso mean: 38.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5144 0 96 103 5343
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5

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