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- PDB-3k1w: New Classes of Potent and Bioavailable Human Renin Inhibitors -

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Basic information

Entry
Database: PDB / ID: 3k1w
TitleNew Classes of Potent and Bioavailable Human Renin Inhibitors
ComponentsRenin
KeywordsHYDROLASE / Renin / protease / Alternative splicing / Aspartyl protease / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Glycoprotein / Membrane / Polymorphism / Secreted / Zymogen
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 / amyloid-beta metabolic process / angiotensin maturation ...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 / amyloid-beta metabolic process / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / 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
Chem-BFX / FORMIC ACID / 2-acetylamino-2-deoxy-alpha-L-idopyranose / Renin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPrade, L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: New classes of potent and bioavailable human renin inhibitors
Authors: Remen, L. / Bezencon, O. / Richard-Bildstein, S. / Bur, D. / Prade, L. / Corminboeuf, O. / Boss, C. / Grisostomi, C. / Sifferlen, T. / Strickner, P. / Hess, P. / Delahaye, S. / Treiber, A. / ...Authors: Remen, L. / Bezencon, O. / Richard-Bildstein, S. / Bur, D. / Prade, L. / Corminboeuf, O. / Boss, C. / Grisostomi, C. / Sifferlen, T. / Strickner, P. / Hess, P. / Delahaye, S. / Treiber, A. / Weller, T. / Binkert, C. / Steiner, B. / Fischli, W.
History
DepositionSep 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)76,5769
Polymers74,8102
Non-polymers1,7667
Water11,295627
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2704
Polymers37,4051
Non-polymers8653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3065
Polymers37,4051
Non-polymers9014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-8 kcal/mol
Surface area28410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.028, 88.697, 118.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO cell / Production host: Homo sapiens (human) / References: UniProt: P00797, renin

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Sugars , 2 types, 2 molecules

#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#6: Sugar ChemComp-HSQ / 2-acetylamino-2-deoxy-alpha-L-idopyranose


Type: L-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
LIdopNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-L-idopyranosamineCOMMON NAMEGMML 1.0
a-L-IdopNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
IdoNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 632 molecules

#2: Chemical ChemComp-BFX / 4-{4-[3-(2-bromo-5-fluorophenoxy)propyl]phenyl}-N-(2-chlorobenzyl)-N-cyclopropyl-1,2,5,6-tetrahydropyridine-3-carboxamide


Mass: 597.945 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H31BrClFN2O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.75
Details: 20-30% PEG 4000, 0.6M KCl, 0.1M NaCitrate buffer, pH 4.75, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 17, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→31.8 Å / Num. all: 98559 / Num. obs: 98559 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→31.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.345 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.093 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 4930 5 %RANDOM
Rwork0.1986 ---
all0.20036 93558 --
obs0.20036 93558 88.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.296 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.97 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5252 0 111 627 5990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225509
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9637493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7725687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36123.946223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23915868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4181520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024184
X-RAY DIFFRACTIONr_nbd_refined0.2110.22484
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23802
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2526
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.237
X-RAY DIFFRACTIONr_mcbond_it1.65233373
X-RAY DIFFRACTIONr_mcangle_it2.62145458
X-RAY DIFFRACTIONr_scbond_it2.21632175
X-RAY DIFFRACTIONr_scangle_it3.32352029
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 263 -
Rwork0.317 5458 -
obs--70.3 %

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