4BZS | pdb_00004bzs

Human angiotenisn converting enzyme N-domain in complex with K-26


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.277 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Interkingdom Pharmacology of Angiotensin-I Converting Enzyme Inhibitor Phosphonates Produced by Actinomycetes

Kramer, G.J.Mohd, A.Schwager, S.L.U.Masuyer, G.Acharya, K.R.Sturrock, E.D.Bachmann, B.O.

(2014) ACS Med Chem Lett 5: 346

  • DOI: https://doi.org/10.1021/ml4004588
  • Primary Citation Related Structures: 
    4BZR, 4BZS

  • PubMed Abstract: 

    The K-26 family of bacterial secondary metabolites are N-modified tripeptides terminated by an unusual phosphonate analog of tyrosine. These natural products, produced via three different actinomycetales, are potent inhibitors of human angiotensin-I converting enzyme (ACE). Herein we investigate the interkingdom pharmacology of the K-26 family by synthesizing these metabolites and assessing their potency as inhibitors of both the N-terminal and C-terminal domains of human ACE. In most cases, selectivity for the C-terminal domain of ACE is displayed. Co-crystallization of K-26 in both domains of human ACE reveals the structural basis of the potent inhibition and has shown an unusual binding motif that may guide future design of domain-selective inhibitors. Finally, the activity of K-26 is assayed against a cohort of microbially produced ACE relatives. In contrast to the synthetic ACE inhibitor captopril, which demonstrates broad interkingdom inhibition of ACE-like enzymes, K-26 selectively targets the eukaryotic family.


  • Organizational Affiliation
    • Vanderbilt University Department of Chemistry, 7300 Stevenson Center, Nashville, Tennessee 37204, United States.

Macromolecule Content 

  • Total Structure Weight: 150.57 kDa 
  • Atom Count: 10,447 
  • Modeled Residue Count: 1,222 
  • Deposited Residue Count: 1,258 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ANGIOTENSIN-CONVERTING ENZYME
A, B
629Homo sapiensMutation(s): 1 
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 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-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G86851RC
GlyCosmos: G86851RC
GlyGen: G86851RC
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, G
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, H
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K26

Query on K26



Download:Ideal Coordinates CCD File
N [auth A],
U [auth B]
N-ACETYL-L-ILE-L-TYR-(R)-1-AMINO-2-(4-HYDROXYPHENYL)ETHYLPHOSPHONIC ACID
C25 H34 N3 O8 P
ZFRNBYWFOLDQKG-FDMHNHSTSA-N
PE4

Query on PE4



Download:Ideal Coordinates CCD File
K [auth A]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
P6G

Query on P6G



Download:Ideal Coordinates CCD File
L [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
V [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
9X6

Query on 9X6



Download:Ideal Coordinates CCD File
O [auth A],
W [auth B]
thiodiglycolic acid
C4 H6 O4 S
UVZICZIVKIMRNE-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
M [auth A],
R [auth B],
S [auth B],
T [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
I [auth A],
P [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
J [auth A],
Q [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.277 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.005α = 88.69
b = 77.32β = 64.53
c = 82.07γ = 75.29
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references
  • Version 1.2: 2018-02-07
    Changes: Advisory, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Structure summary