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- PDB-3own: Potent macrocyclic renin inhibitors -

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Basic information

Entry
Database: PDB / ID: 3own
TitlePotent macrocyclic renin inhibitors
ComponentsRenin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / RENIN / PROTEASE / ASPARTYL PROTEASE / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / response to immobilization stress / regulation of MAPK cascade / response to cAMP / amyloid-beta metabolic process ...renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / response to immobilization stress / regulation of MAPK cascade / response to cAMP / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins / cell maturation / angiotensin maturation / hormone-mediated signaling pathway / insulin-like growth factor receptor binding / 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
Chem-3OW / Chem-3OX / ACETATE ION / Renin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBorkakoti, N. / Derbyshire, D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Design and synthesis of potent macrocyclic renin inhibitors.
Authors: Sund, C. / Belda, O. / Wiktelius, D. / Sahlberg, C. / Vrang, L. / Sedig, S. / Hamelink, E. / Henderson, I. / Agback, T. / Jansson, K. / Borkakoti, N. / Derbyshire, D. / Eneroth, A. / Samuelsson, B.
History
DepositionSep 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)76,4199
Polymers74,8102
Non-polymers1,6097
Water6,179343
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3217
Polymers37,4051
Non-polymers9166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0982
Polymers37,4051
Non-polymers6931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Renin
hetero molecules

A: Renin
hetero molecules

A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,96321
Polymers112,2153
Non-polymers2,74818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6410 Å2
ΔGint-79 kcal/mol
Surface area38390 Å2
MethodPISA
4
B: Renin
hetero molecules

B: Renin
hetero molecules

B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2946
Polymers112,2153
Non-polymers2,0793
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4200 Å2
ΔGint-33 kcal/mol
Surface area38660 Å2
MethodPISA
5
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)229,25727
Polymers224,4316
Non-polymers4,82721
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area16810 Å2
ΔGint-117 kcal/mol
Surface area70860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.827, 141.827, 141.827
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-802-

NA

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Renin / Angiotensinogenase


Mass: 37405.152 Da / Num. of mol.: 2 / Fragment: UNP residues 67-406 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00797, renin

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Non-polymers , 5 types, 350 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-3OX / (2S,4S)-4-hydroxy-2-(1-methylethyl)-4-[(4R,13S)-18-[methyl(methylsulfonyl)amino]-2,15-dioxo-4-phenyl-11-oxa-3,14-diazatricyclo[14.3.1.1~5,9~]henicosa-1(20),5(21),6,8,16,18-hexaen-13-yl]-N-(2-methylpropyl)butanamide


Mass: 692.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H48N4O7S
#5: Chemical ChemComp-3OW / (2S,4S)-4-hydroxy-2-(1-methylethyl)-4-[(4S,13S)-18-[methyl(methylsulfonyl)amino]-2,15-dioxo-4-phenyl-11-oxa-3,14-diazatricyclo[14.3.1.1~5,9~]henicosa-1(20),5(21),6,8,16,18-hexaen-13-yl]-N-(2-methylpropyl)butanamide


Mass: 692.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H48N4O7S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growTemperature: 299 K / Method: vapor diffusion / Details: vapor diffusion, temperature 299K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→70.913 Å / Num. all: 64051 / Num. obs: 64051 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.115.50.5311.45101892810.531100
2.11-2.245.40.4161.74776887960.416100
2.24-2.395.40.2742.54516683150.274100
2.39-2.585.60.1813.94308377050.181100
2.58-2.835.60.1444.53989871310.144100
2.83-3.165.60.1155.43580564450.115100
3.16-3.655.50.1045.93150457460.104100
3.65-4.475.30.115.42589248430.1199.9
4.47-6.325.20.0975.71943737610.09799.1
6.32-70.9135.40.0826.71086420280.08293.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→70.89 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 4.043 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 3227 5.1 %RANDOM
Rwork0.2168 ---
obs0.2187 63618 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.05 Å2 / Biso mean: 24.5479 Å2 / Biso min: 3 Å2
Refinement stepCycle: LAST / Resolution: 2→70.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 112 343 5603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225392
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.9787320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24424.091220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46615854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.131520
X-RAY DIFFRACTIONr_chiral_restr0.1290.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024088
X-RAY DIFFRACTIONr_nbd_refined0.220.22441
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2372
X-RAY DIFFRACTIONr_metal_ion_refined0.030.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0850.22
X-RAY DIFFRACTIONr_mcbond_it1.1221.53310
X-RAY DIFFRACTIONr_mcangle_it2.03225338
X-RAY DIFFRACTIONr_scbond_it3.20932117
X-RAY DIFFRACTIONr_scangle_it4.9134.51982
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 234 -
Rwork0.283 4484 -
all-4718 -
obs--100 %

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