8GJV | pdb_00008gjv

Chemical synthesis of maxamycins: Intermediate compound 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 
    0.132 (Depositor), 0.132 (DCC) 
  • R-Value Work: 
    0.118 (Depositor), 0.118 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8GJV

This is version 4.0 of the entry. See complete history

Literature

Divergent Total Synthesis and Characterization of Maxamycins.

Moore, M.J.Qin, P.Keith, D.J.Wu, Z.C.Jung, S.Chatterjee, S.Tan, C.Qu, S.Cai, Y.Stanfield, R.L.Boger, D.L.

(2023) J Am Chem Soc 145: 12837-12852

  • DOI: https://doi.org/10.1021/jacs.3c03710
  • Primary Citation Related Structures: 
    8GJV

  • PubMed Abstract: 

    A new streamlined and scaled divergent total synthesis of pocket-modified vancomycin analogs is detailed that provides a common late-stage intermediate [Ψ[C(═S)NH]Tpg 4 ]vancomycin (LLS = 18 steps, 12% overall yield, >5 g prepared) to access both existing and future pocket modifications. Highlights of the approach include an atroposelective synthesis of [Ψ[C(═S)NH]Tpg 4 ]vancomycin aglycon ( 11 ), a one-pot enzymatic glycosylation for direct conversion to [Ψ[C(═S)NH]Tpg 4 ]vancomycin ( 12 ), and new powerful methods for the late-stage conversion of the embedded thioamide to amidine/aminomethylene pocket modifications. Incorporation of two peripheral modifications provides a scalable total synthesis of the maxamycins, all prepared from aglycon 11 without use of protecting groups. Thus, both existing and presently unexplored pocket-modified analogues paired with a range of peripheral modifications are accessible from this common thioamide intermediate. In addition to providing an improved synthesis of the initial member of the maxamycins, this is illustrated herein with the first synthesis and examination of maxamycins that contain the most effective of the pocket modifications (amidine) described to date combined with two additional peripheral modifications. These new amidine-based maxamycins proved to be potent, durable, and efficacious antimicrobial agents that display equipotent activity against vancomycin-sensitive and vancomycin-resistant Gram-positive organisms and act by three independent synergistic mechanisms of action. In the first such study conducted to date, one new maxamycin ( 21 , MX-4) exhibited efficacious in vivo activity against a feared and especially challenging multidrug-resistant (MRSA) and vancomycin-resistant (VRSA) S. aureus bacterial strain (VanA VRS-2) for which vancomycin is inactive.

Macromolecule Content 

  • Total Structure Weight: 8.13 kDa 
  • Atom Count: 587 
  • Modeled Residue Count: 32 
  • Deposited Residue Count: 32 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Intermediate compound 10 for maxamycins synthesis
A, B, C, D
8synthetic constructMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MOH

Query on MOH



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
E [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
E [auth A],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A],
MA [auth D],
N [auth B],
NA [auth D],
O [auth B],
OA [auth D],
P [auth B],
PA [auth D],
Q [auth B],
QA [auth D],
R [auth B],
RA [auth D],
S [auth B],
SA [auth D],
T [auth B],
TA [auth D],
U [auth B],
UA [auth D],
V [auth B],
VA [auth D],
W [auth B],
WA [auth D],
X [auth B],
Y [auth B],
Z [auth B]
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
MLU
Query on MLU
A, B, C, D
D-PEPTIDE LINKINGC7 H15 N O2

--

ZRJ
Query on ZRJ
A, B, C, D
L-PEPTIDE LINKINGC14 H21 N O4

--

ZSX
Query on ZSX
A, B, C, D
D-PEPTIDE LINKINGC9 H11 N O3GLY
ZT6
Query on ZT6
A, B, C, D
L-PEPTIDE LINKINGC18 H30 Cl N O4 SiTYR
ZT9
Query on ZT9
A, B, C, D
D-PEPTIDE LINKINGC9 H11 N O2 S

--

ZTG
Query on ZTG
A, B, C, D
D-PEPTIDE LINKINGC18 H30 Cl N O4 Si

--

ZTK
Query on ZTK
A, B, C, D
L-PEPTIDE LINKINGC4 H6 N2 O2ALA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free:  0.132 (Depositor), 0.132 (DCC) 
  • R-Value Work:  0.118 (Depositor), 0.118 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.582α = 90
b = 19.693β = 96.61
c = 51.816γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
APEX 2data reduction
APEX 2data scaling
SHELXTphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Structure summary
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 3.0: 2024-04-17
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 4.0: 2024-09-11
    Changes: Atomic model, Data collection