7Q24 | pdb_00007q24

Crystal structure of Angiotensin-1 converting enzyme N-domain in complex with dual ACE/NEP inhibitor AD011

PDB DOI: https://doi.org/10.2210/pdb7Q24/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): Yes

Deposited: 2021-10-23 Released: 2022-02-16
Deposition Author(s): Cozier, G.E., Acharya, K.R.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.214 (Depositor), 0.213 (DCC)
R-Value Work:
0.185 (Depositor), 0.183 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Probing the Requirements for Dual Angiotensin-Converting Enzyme C-Domain Selective/Neprilysin Inhibition.

Arendse, L.B., Cozier, G.E., Eyermann, C.J., Basarab, G.S., Schwager, S.L., Chibale, K., Acharya, K.R., Sturrock, E.D.

(2022) J Med Chem 65: 3371-3387

PubMed: 35113565 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.1c01924
Primary Citation Related Structures:
7Q24, 7Q25, 7Q26, 7Q27, 7Q28, 7Q29

PubMed Abstract:
Selective inhibition of the angiotensin-converting enzyme C-domain (cACE) and neprilysin (NEP), leaving the ACE N-domain (nACE) free to degrade bradykinin and other peptides, has the potential to provide the potent antihypertensive and cardioprotective benefits observed for nonselective dual ACE/NEP inhibitors, such as omapatrilat, without the increased risk of adverse effects. We have synthesized three 1-carboxy-3-phenylpropyl dipeptide inhibitors with nanomolar potency based on the previously reported C-domain selective ACE inhibitor lisinopril-tryptophan (LisW) to probe the structural requirements for potent dual cACE/NEP inhibition. Here we report the synthesis, enzyme kinetic data, and high-resolution crystal structures of these inhibitors bound to nACE and cACE, providing valuable insight into the factors driving potency and selectivity. Overall, these results highlight the importance of the interplay between the S ₁' and S ₂' subsites for ACE domain selectivity, providing guidance for future chemistry efforts toward the development of dual cACE/NEP inhibitors.

Organizational Affiliation

Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa.

Macromolecule Content

Total Structure Weight: 151.12 kDa
Atom Count: 10,964
Modeled Residue Count: 1,215
Deposited Residue Count: 1,258
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme	A, B	629	Homo sapiens	Mutation(s): 8 Gene Names: ACE, DCP, DCP1 EC: 3.2.1 (PDB Primary Data), 3.4.15.1 (PDB Primary Data)
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12821
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P12821-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	D, F	4		N-Glycosylation	Interactions Focus chain D Focus chain F Interactions & Density Focus chain D Focus chain F
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G	2		N-Glycosylation	Interactions Focus chain E Focus chain G Interactions & Density Focus chain E Focus chain G
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8KC (Subject of Investigation/LOI) Query on 8KC Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain S [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain S [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain S [auth A]	EA [auth B], S [auth A]	(2~{S})-2-[[(2~{S})-1-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-hexan-2-yl]amino]-4-phenyl-butanoic acid C₂₇ H₃₃ N₃ O₅ YWBHCYRCVYEOPE-HJOGWXRNSA-N		Interactions Focus chain EA [auth B] Focus chain S [auth A] Interactions & Density Focus chain EA [auth B] Focus chain S [auth A]
P33 Query on P33 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B] mmCIF format, chain U [auth B]	U [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain W [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth B] mmCIF format, chain T [auth B] mmCIF format, chain W [auth B]	T [auth B], W [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Focus chain W [auth B] Interactions & Density Focus chain T [auth B] Focus chain W [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A]	AA [auth B], H [auth A], I [auth A], K [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Interactions & Density Focus chain AA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain P [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain P [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain P [auth A]	BA [auth B], P [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain P [auth A] Interactions & Density Focus chain BA [auth B] Focus chain P [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain V [auth B] SDF format, chain Y [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth B]	M [auth A], O [auth A], V [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain O [auth A] Focus chain V [auth B] Focus chain Y [auth B] Interactions & Density Focus chain M [auth A] Focus chain O [auth A] Focus chain V [auth B] Focus chain Y [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain X [auth B] SDF format, chain Z [auth B] MOL2 format, chain L [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain L [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth B]	L [auth A], X [auth B], Z [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain X [auth B] Focus chain Z [auth B] Interactions & Density Focus chain L [auth A] Focus chain X [auth B] Focus chain Z [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain Q [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain Q [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain Q [auth A]	CA [auth B], Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth B] Focus chain Q [auth A] Interactions & Density Focus chain CA [auth B] Focus chain Q [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain R [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain R [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain R [auth A]	DA [auth B], R [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain R [auth A] Interactions & Density Focus chain DA [auth B] Focus chain R [auth A]