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- PDB-9h1c: Crystal structure of Angiotensin-1 converting enzyme C-domain in ... -

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Basic information

Entry
Database: PDB / ID: 9h1c
TitleCrystal structure of Angiotensin-1 converting enzyme C-domain in complex with dual ACE/NEP inhibitor AD014
ComponentsAngiotensin-converting enzyme
KeywordsHYDROLASE / Angiotensin-1 converting enzyme / Dual inhibitor / NEP / Metalloprotease
Function / homology
Function and homology information


mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / positive regulation of peptidyl-cysteine S-nitrosylation ...mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / positive regulation of peptidyl-cysteine S-nitrosylation / negative regulation of calcium ion import / response to laminar fluid shear stress / negative regulation of gap junction assembly / metallodipeptidase activity / cellular response to aldosterone / hormone catabolic process / bradykinin catabolic process / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / negative regulation of D-glucose import / vasoconstriction / neutrophil mediated immunity / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / hormone metabolic process / mitogen-activated protein kinase binding / embryo development ending in birth or egg hatching / chloride ion binding / mitogen-activated protein kinase kinase binding / positive regulation of neurogenesis / arachidonate secretion / post-transcriptional regulation of gene expression / eating behavior / heterocyclic compound binding / peptide catabolic process / heart contraction / lung alveolus development / antigen processing and presentation of peptide antigen via MHC class I / regulation of heart rate by cardiac conduction / positive regulation of systemic arterial blood pressure / response to dexamethasone / regulation of systemic arterial blood pressure by renin-angiotensin / blood vessel remodeling / hematopoietic stem cell differentiation / amyloid-beta metabolic process / regulation of vasoconstriction / peptidyl-dipeptidase activity / animal organ regeneration / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / positive regulation of vasoconstriction / carboxypeptidase activity / sperm midpiece / blood vessel diameter maintenance / basal plasma membrane / kidney development / angiotensin-activated signaling pathway / female pregnancy / brush border membrane / response to nutrient levels / cellular response to glucose stimulus / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / male gonad development / metallopeptidase activity / peptidase activity / actin binding / spermatogenesis / endopeptidase activity / response to lipopolysaccharide / lysosome / response to hypoxia / calmodulin binding / endosome / positive regulation of apoptotic process / response to xenobiotic stimulus / external side of plasma membrane / negative regulation of gene expression / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
: / BORIC ACID / IMIDAZOLE / TRIETHYLENE GLYCOL / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCozier, G.E. / Acharya, K.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X001032/1 United Kingdom
Citation
Journal: J.Med.Chem. / Year: 2025
Title: Design of Novel Mercapto-3-phenylpropanoyl Dipeptides as Dual Angiotensin-Converting Enzyme C-Domain-Selective/Neprilysin Inhibitors.
Authors: Cozier, G.E. / Coulson, L.B. / Eyermann, C.J. / Basarab, G.S. / Schwager, S.L. / Chibale, K. / Sturrock, E.D. / Acharya, K.R.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,25014
Polymers68,8621
Non-polymers2,38813
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint17 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.728, 84.744, 134.425
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Angiotensin-converting enzyme / ACE / Dipeptidyl carboxypeptidase I / Kininase II


Mass: 68861.875 Da / Num. of mol.: 1 / Mutation: E64G, N90Q, N155Q, N337Q, N586Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE, DCP, DCP1 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P12821, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, peptidyl-dipeptidase A

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#8: 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.: 1 / 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

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Non-polymers , 8 types, 512 molecules

#3: Chemical ChemComp-A1IRQ / (2~{S},5~{R})-5-(3-hydroxyphenyl)-1-[2-[[(2~{S})-3-(4-hydroxyphenyl)-2-sulfanyl-propanoyl]amino]ethanoyl]pyrrolidine-2-carboxylic acid


Mass: 444.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N2O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BH3O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M MIB pH 4.0, 5% glycerol, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.8→84.74 Å / Num. obs: 61018 / % possible obs: 100 % / Redundancy: 21.5 % / Biso Wilson estimate: 20.44 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.286 / Rpim(I) all: 0.063 / Net I/σ(I): 10
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 21.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3580 / CC1/2: 0.574 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→71.69 Å / SU ML: 0.2099 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.9456
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 2054 3.39 %
Rwork0.171 58522 -
obs0.1723 60576 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.54 Å2
Refinement stepCycle: LAST / Resolution: 1.8→71.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4777 0 154 501 5432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415118
X-RAY DIFFRACTIONf_angle_d0.75816959
X-RAY DIFFRACTIONf_chiral_restr0.0412745
X-RAY DIFFRACTIONf_plane_restr0.0065890
X-RAY DIFFRACTIONf_dihedral_angle_d14.04971887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.30881240.27843851X-RAY DIFFRACTION98.86
1.84-1.890.33631130.253866X-RAY DIFFRACTION98.98
1.89-1.940.27691490.23523819X-RAY DIFFRACTION99.5
1.94-20.28631390.21893828X-RAY DIFFRACTION99.57
2-2.060.23761300.21693882X-RAY DIFFRACTION99.88
2.06-2.130.22051420.17543870X-RAY DIFFRACTION99.83
2.13-2.220.2341230.16973876X-RAY DIFFRACTION99.28
2.22-2.320.20941510.16553860X-RAY DIFFRACTION99.36
2.32-2.440.21081290.16743877X-RAY DIFFRACTION99.18
2.44-2.60.23161510.16043851X-RAY DIFFRACTION99.21
2.6-2.80.24861530.17163884X-RAY DIFFRACTION99.61
2.8-3.080.1971220.16663938X-RAY DIFFRACTION99.71
3.08-3.520.19381410.16143969X-RAY DIFFRACTION99.81
3.52-4.440.17151340.13554000X-RAY DIFFRACTION99.93
4.44-71.690.17431530.16124151X-RAY DIFFRACTION99.65
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)
11.94720184340.576623839835-0.2372604413473.82560544767-4.329492786234.85067998195-0.2676032177670.158681118774-0.150555426529-0.3682580652510.121942118586-0.3772902318210.0399792160792-0.2136476040430.1500922717830.214801760494-0.05444103627860.03170245115340.334459367296-0.01969083810890.166120690624-11.07910248956.697113882510.728100078682
23.118221373350.673247964476-0.4404584222022.06981984426-0.8563806798221.7466942196-0.2711740124650.20191693269-0.126839598758-0.2479315982950.0727887283521-0.1543371520850.0128976331002-0.007395734328680.1681800729370.236557200201-0.01142461464040.01773381402240.2490899953260.008617430580760.121971078247-3.702750120327.377100561744.22850862883
30.7923676284780.447903744167-0.445558233672.11670884744-0.7098591747491.15326828165-0.04438132656310.0919038889241-0.110166643133-0.309964810124-0.0340673024082-0.06311784975260.1976085584950.01380884708810.07955055245670.147804593214-0.00664047035066-0.00454848228330.163414536024-0.02318509381820.115213584924-0.492230162015-12.141829161320.2305979607
40.804343011988-0.237390159318-0.5243683618884.81034890639-2.886896736643.99816958138-0.02583361346460.02794049815690.08031200486490.548606937040.0886463212536-0.0562281016487-0.374728664471-0.036486722363-0.06261225537460.08817319814420.00370608884196-0.003980707812540.1470986865380.001685869249420.0888192278255-10.26340891-6.0593341249842.8765327243
52.72111105771-0.695731878732-0.5387029173661.35837808684-0.6065868442120.994952957687-0.008606964722060.00151603038968-0.122941950990.1179322796480.05013292774340.1633060676590.0980768508345-0.175984458493-0.03062439116660.151299810612-0.008837932919160.01340366846460.11727685783-0.007043947796470.0997523792412-14.0083634577-18.506131760240.6868366723
62.077201613020.862448080944-0.8787000664452.15795985153-0.7415677382722.08964535163-0.2934703292040.266279097359-0.484155848391-0.3622928162130.128691531284-0.2456606463570.415333581842-0.1344548096150.1285680060780.232248635617-0.03252901326790.05718484601170.219199066367-0.04287238518680.232476857231-24.0045799907-10.920016820114.7507218093
72.47834338090.754718442676-0.5058461752962.97952637476-0.01242753160090.690456277130.07374067907360.0263986987673-0.0720310941875-0.0188547972275-0.06211119766470.1598170233660.00159835955799-0.0701620268539-0.02155651664660.1091549118110.0184332437932-0.01973375239880.1490994770520.008091072598140.121417144503-25.9542113727-2.9702022032923.9555188736
81.121510590250.305304041571-0.8100854576280.986562930442-0.5086843159721.67550679497-0.02050094765360.0303111690557-0.01273682899490.07250486083170.007660577815-0.035217262242-0.01331170323180.02342976463320.005460504592940.09515541107510.007870256072020.0006015224280760.1007828009820.001938173568830.0800738854079-3.96364751038-8.4140792141832.1626087817
93.07553375194-0.0618940589418-0.2614820357071.52916134142-0.4883470354851.678104253610.005655079850150.006786077138820.1114504966470.060995904230.0652491510030.230451559756-0.12685050256-0.205777946586-0.07823234228130.131130578370.02364423398530.02539815804410.1238341007920.01701365984420.152894039468-25.67979175815.8050708093827.4388242977
100.9659758212790.1987312022040.4338589176782.67477449269-2.096699695962.656435557130.108540110544-0.105082408095-0.1166887350240.260852072075-0.005763794055450.0415728874042-0.03817300911660.0808647127639-0.09106446609590.1886030481790.009193509162510.01744141316690.169194662385-0.04269776532950.0918947867529-13.0793494518-5.6752996836846.3025062929
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 40 through 70 )40 - 701 - 31
22chain 'A' and (resid 71 through 128 )71 - 12832 - 89
33chain 'A' and (resid 129 through 228 )129 - 22890 - 189
44chain 'A' and (resid 229 through 259 )229 - 259190 - 220
55chain 'A' and (resid 260 through 300 )260 - 300221 - 261
66chain 'A' and (resid 301 through 393 )301 - 393262 - 354
77chain 'A' and (resid 394 through 439 )394 - 439355 - 400
88chain 'A' and (resid 440 through 520 )440 - 520401 - 481
99chain 'A' and (resid 521 through 582 )521 - 582482 - 543
1010chain 'A' and (resid 583 through 625 )583 - 625544 - 586

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