9SGD | pdb_00009sgd

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (26)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 
    0.205 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.189 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure-Activity Relationship and Crystallographic Study of New Monobactams.

Kavas, V.Contreras-Martel, C.Pajk, S.Knez, D.Martins, A.Gould, T.A.Roper, D.I.Zdovc, I.Dessen, A.Hrast Rambaher, M.Gobec, S.

(2026) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02427
  • Primary Citation of Related Structures:  
    9SG5, 9SG6, 9SG7, 9SG8, 9SG9, 9SGA, 9SGB, 9SGC, 9SGD, 9SGE

  • PubMed Abstract: 

    Monobactams, a subclass of β-lactam antibiotics with a monocyclic scaffold, are uniquely resistant to hydrolysis by metallo-β-lactamases, providing a distinct therapeutic advantage. Here, we report an in silico -based structure-activity relationship (SAR) investigation of aztreonam-related monobactams. A focused library of monobactam derivatives was synthesized and evaluated for inhibition of penicillin-binding proteins (PBPs) and antibacterial activity. Ten compounds, including aztreonam, were crystallized with truncated PBP1b from Streptococcus pneumoniae , used as a model PBP. Potent PBP1b inhibitors were developed, although high enzymatic potency was not always reflected in strong antibacterial activity. Certain derivatives showed activity against Staphylococcus aureus , which is typically resistant to monobactams. 2D similarity search identified potent inhibitors active against Escherichia coli , Klebsiella pneumoniae , and Acinetobacter baumannii . Crystal structures revealed previously unrecognized binding interactions, including a halogen bond with a conserved threonine residue, underscoring the potential of these interactions to support the development of more potent PBP inhibitors.


  • Organizational Affiliation
    • Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein 1B494Streptococcus pneumoniaeMutation(s): 3 
Gene Names: pbp1b
UniProt
Find proteins for O70038 (Streptococcus pneumoniae)
Explore O70038 
Go to UniProtKB:  O70038
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO70038
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JNT (Subject of Investigation/LOI)
Query on A1JNT

Download Ideal Coordinates CCD File 
B [auth A][(2~{S},3~{S})-3-[[2-(2-azanyl-1,3-thiazol-4-yl)-2-(2-methoxy-2-oxidanylidene-ethoxy)imino-ethanoyl]amino]-4-oxidanylidene-butan-2-yl]sulfamic acid
C12 H17 N5 O8 S2
JSCREYWKSPYSLM-NKWVEPMBSA-N
TAU
Query on TAU

Download Ideal Coordinates CCD File 
EA [auth A]2-AMINOETHANESULFONIC ACID
C2 H7 N O3 S
XOAAWQZATWQOTB-UHFFFAOYSA-N
SO3
Query on SO3

Download Ideal Coordinates CCD File 
C [auth A]SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
D [auth A]
DA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
D [auth A],
DA [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free:  0.205 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.189 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.239α = 90
b = 148.297β = 90
c = 98.144γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Slovenian Research AgencySloveniaP1-0208
Slovenian Research AgencySloveniaJ1-50039
Slovenian Research AgencySloveniaJ3-50123
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-05-02
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)FranceANR-17-EURE-0003

Revision History  (Full details and data files)

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