9CSG | pdb_00009csg

Human Serum Albumin Bound to Cerastecin Compound 5e


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.262 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9CSG

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Cerastecin Inhibition of the Lipooligosaccharide Transporter MsbA to Combat Acinetobacter baumannii : From Screening Impurity to In Vivo Efficacy.

Skudlarek, J.W.Cooke, A.J.Mitchell, H.J.Babaoglu, K.Shaw, A.W.Tong, L.Nomland, A.B.Labroli, M.Sha, D.Mulhearn, J.J.Wu, C.Li, S.W.Beshore, D.C.Hughes, J.M.E.Jouffroy, M.Wang, H.Balibar, C.J.Painter, R.E.Shen, P.Lange, H.S.Ishchenko, A.Chen, Y.T.Klein, D.J.Tracy, R.W.Miller, R.R.Cabalu, T.D.Wu, Z.Leithead, A.Scapin, G.Hruza, A.W.Dzhekieva, L.Bukhtiyarova, M.Homsher, M.F.Xu, M.Bahnck-Teets, C.McKenney, D.Buevich, A.V.Liu, J.Zhang, L.K.Meng, T.Kelly, T.DiNunzio, E.Soisson, S.Cheng, R.K.Y.Hennig, M.Raheem, I.Walker, S.S.

(2024) J Med Chem 67: 15620-15675

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01277
  • Primary Citation Related Structures: 
    9CSG, 9CSI

  • PubMed Abstract: 

    Acinetobacter baumannii , a commonly multidrug-resistant Gram-negative bacterium responsible for large numbers of bloodstream and lung infections worldwide, is increasingly difficult to treat and constitutes a growing threat to human health. Structurally novel antibacterial chemical matter that can evade existing resistance mechanisms is essential for addressing this critical medical need. Herein, we describe our efforts to inhibit the essential A. baumannii lipooligosaccharide (LOS) ATP-binding cassette (ABC) transporter MsbA. An unexpected impurity from a phenotypic screening was optimized as a series of dimeric compounds, culminating with 1 (cerastecin D), which exhibited antibacterial activity in the presence of human serum and a pharmacokinetic profile sufficient to achieve efficacy against A. baumannii in murine septicemia and lung infection models.


  • Organizational Affiliation
    • Merck & Co., Inc., Rahway, New Jersey 07065, United States.

Macromolecule Content 

  • Total Structure Weight: 68.42 kDa 
  • Atom Count: 5,023 
  • Modeled Residue Count: 582 
  • Deposited Residue Count: 582 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Albumin582Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens)
Explore P02768 
Go to UniProtKB:  P02768
PHAROS:  P02768
GTEx:  ENSG00000163631 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02768
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AZR
(Subject of Investigation/LOI)

Query on A1AZR



Download:Ideal Coordinates CCD File
H [auth A]2-(4-butylbenzene-1-sulfonamido)-5-(4-{3-carboxy-4-[4-(2-methoxyethyl)benzene-1-sulfonamido]anilino}-4-oxobutanamido)benzoic acid
C37 H40 N4 O11 S2
ZUDKFHHJONZZCP-UHFFFAOYSA-N
MYR

Query on MYR



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.262 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.647α = 90
b = 38.624β = 104.89
c = 97.78γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-09-25
    Changes: Database references
  • Version 1.2: 2024-10-02
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Structure summary