9SSB | pdb_00009ssb

Human angiotensin 1-converting enzyme N-domain in complex with zofenoprilat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.226 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.207 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Kinetic and structural characterisation of domain-specific angiotensin I-converting enzyme inhibition by captopril, rentiapril and zofenoprilat.

Gregory, K.S.Ramasamy, V.Sturrock, E.D.Acharya, K.R.

(2026) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70428
  • Primary Citation Related Structures: 
    9SS7, 9SS8, 9SS9, 9SSA, 9SSB

  • PubMed Abstract: 

    Angiotensin I-converting enzyme (ACE) is a zinc-dependent dipeptidyl carboxypeptidase involved in blood pressure regulation through proteolysis of angiotensin I (Ang-I) into the potent vasoconstrictor, angiotensin II (Ang-II). Inhibition of ACE is therefore used for the treatment of hypertension, heart failure, myocardial infarction, stroke and chronic kidney disease. Current ACE inhibitors (ACEi) bind both the N- and C-catalytic domains of ACE (referred to as nACE and cACE), and this has been linked to the occurrence of side effects due to the wide substrate specificity of ACE. The development of domain selective ACEi with reduced side effects is therefore key for improved therapeutic intervention. Understanding how current ACEi bind nACE and cACE, and their differences in domain selectivity should aid structure-based development of more selective ACEi by identifying different chemical groups that increase or decrease selectivity. We present the kinetic and structural characterisation of nACE and cACE with three thiolate ACEi, captopril (K i , nACE = 2.53 nm and cACE = 2.04 nm), rentiapril (monomer K i , nACE = 2.22 nm and cACE = 6.77 nm) and zofenoprilat (K i , nACE = 2.86 nm and cACE = 0.61 nm). Detailed structural analysis indicated that the S2' subsite likely contributes to the variation in domain selectivity observed for rentiapril and zofenoprilat due to differences in hydrophobicity and displacement of water molecules that contribute to ACE's hydration shell. Interestingly, in the cACE crystal structure, rentiapril bound as a dimer, and kinetic data revealed that both the monomeric and dimeric (dimer K i , nACE = 15.11 nm and cACE = 36.38 nm) forms of rentiapril inhibit ACE with nanomolar affinity.


  • Organizational Affiliation
    • Department of Life Sciences, University of Bath, UK.

Macromolecule Content 

  • Total Structure Weight: 302.12 kDa 
  • Atom Count: 21,759 
  • Modeled Residue Count: 2,422 
  • Deposited Residue Count: 2,512 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme, soluble form
A, B, C, D
628Homo sapiensMutation(s): 0 
Gene Names: ACEDCPDCP1
EC: 3.4.15.1
UniProt & NIH Common Fund Data Resources
Find proteins for P12821 (Homo sapiens)
Explore P12821 
Go to UniProtKB:  P12821
PHAROS:  P12821
GTEx:  ENSG00000159640 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12821
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P12821-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseE,
F [auth K],
G [auth M]
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G47477HI
GlyCosmos: G47477HI
GlyGen: G47477HI
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth N],
N [auth H],
O [auth Q]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G86851RC
GlyCosmos: G86851RC
GlyGen: G86851RC
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth O]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth P]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G62182OO
GlyCosmos: G62182OO
GlyGen: G62182OO
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth F],
L [auth G],
M [auth R]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
12P

Query on 12P



Download:Ideal Coordinates CCD File
EA [auth A]DODECAETHYLENE GLYCOL
C24 H50 O13
WRZXKWFJEFFURH-UHFFFAOYSA-N
XPE

Query on XPE



Download:Ideal Coordinates CCD File
TA [auth C]3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
C20 H42 O11
DTPCFIHYWYONMD-UHFFFAOYSA-N
PE8

Query on PE8



Download:Ideal Coordinates CCD File
HA [auth B]3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
ZED
(Subject of Investigation/LOI)

Query on ZED



Download:Ideal Coordinates CCD File
GA [auth B],
IB [auth D],
Q [auth A],
SA [auth C]
L-PROLINE, 1-[(2S)-3-MERCAPTO-2-METHYL-1-OXOPROPYL]-4-(PHENYLTHIO)-, 4S
C15 H19 N O3 S2
UQWLOWFDKAFKAP-WXHSDQCUSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
CA [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
KB [auth D]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
AA [auth A],
EB [auth C],
PB [auth D]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
OA [auth B],
VA [auth C]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG

Query on PEG



Download:Ideal Coordinates CCD File
IA [auth B]
KA [auth B]
MB [auth D]
R [auth A]
T [auth A]
IA [auth B],
KA [auth B],
MB [auth D],
R [auth A],
T [auth A],
WA [auth C],
X [auth A],
XA [auth C],
YA [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
FA [auth B],
HB [auth D],
P [auth A],
RA [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AB [auth C]
BB [auth C]
CB [auth C]
DB [auth C]
JA [auth B]
AB [auth C],
BB [auth C],
CB [auth C],
DB [auth C],
JA [auth B],
JB [auth D],
LA [auth B],
LB [auth D],
MA [auth B],
NA [auth B],
S [auth A],
UA [auth C],
V [auth A],
W [auth A],
Y [auth A],
Z [auth A],
ZA [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
U [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
BA [auth A],
FB [auth C],
NB [auth D],
PA [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
DA [auth A],
GB [auth C],
OB [auth D],
QA [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.226 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.207 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.532α = 84.902
b = 101.88β = 85.457
c = 114.274γ = 81.349
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/X001032/1

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-18
    Type: Initial release