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- PDB-7xgk: Human renin in complex with compound1 -

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Basic information

Entry
Database: PDB / ID: 7xgk
TitleHuman renin in complex with compound1
ComponentsRenin
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX
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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Unknown ligand / Renin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsKashima, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Discovery of Novel 2-Carbamoyl Morpholine Derivatives as Highly Potent and Orally Active Direct Renin Inhibitors.
Authors: Iijima, D. / Sugama, H. / Awai, N. / Takahashi, Y. / Togashi, Y. / Takebe, T. / Xie, J. / Shen, J. / Ke, Y. / Akatsuka, H. / Kawaguchi, T. / Takedomi, K. / Kashima, A. / Nishio, M. / Inui, Y. ...Authors: Iijima, D. / Sugama, H. / Awai, N. / Takahashi, Y. / Togashi, Y. / Takebe, T. / Xie, J. / Shen, J. / Ke, Y. / Akatsuka, H. / Kawaguchi, T. / Takedomi, K. / Kashima, A. / Nishio, M. / Inui, Y. / Yoneda, H. / Xia, G. / Iijima, T.
History
DepositionApr 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release

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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)74,9766
Polymers74,5342
Non-polymers4424
Water1,17165
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4883
Polymers37,2671
Non-polymers2212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint5 kcal/mol
Surface area15100 Å2
MethodPISA
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4883
Polymers37,2671
Non-polymers2212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint5 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.340, 141.340, 141.340
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Cell line (production host): HEK293 / 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: obtained synthetically / 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-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50mM Na citrate pH4.5, 18-26% PEG3350, 0.6M NaCl

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→49.97 Å / Num. obs: 36921 / % possible obs: 99.7 % / Redundancy: 53.198 % / Biso Wilson estimate: 57.665 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.315 / Rrim(I) all: 0.318 / Χ2: 0.973 / Net I/σ(I): 15.22 / Num. measured all: 1964140 / Scaling rejects: 336
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.5651.8274.6331.75329726644863620.6564.67898.7
2.56-2.7355.2552.5153.3292632529852960.8782.539100
2.73-2.9552.8771.2576.13273320517151690.9621.269100
2.95-3.2354.0210.67110.8254495471147110.9860.677100
3.23-3.6154.910.32819.06236387430543050.9960.331100
3.61-4.1651.8340.1927.49196245378637860.9970.192100
4.16-5.0954.5150.14435.35177393325432540.9980.145100
5.09-7.1551.1090.13735.15129714253825380.9980.138100
7.15-49.9749.4850.11240.1874228150615000.9980.11499.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→49.97 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.468 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 1846 5 %RANDOM
Rwork0.2017 ---
obs0.2039 35074 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.22 Å2 / Biso mean: 52.785 Å2 / Biso min: 22.39 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.4→49.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5242 0 82 65 5389
Biso mean--62.85 40.3 -
Num. residues----680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135456
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174926
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.6527408
X-RAY DIFFRACTIONr_angle_other_deg1.2741.57411458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9975678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57222.927246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28315872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5531520
X-RAY DIFFRACTIONr_chiral_restr0.0670.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021148
LS refinement shellResolution: 2.401→2.464 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 132 -
Rwork0.351 2523 -
all-2655 -
obs--99.1 %

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