3S1Y

AMP-C BETA-LACTAMASE (PSEUDOMONAS AERUGINOSA) in complex with a beta-lactamase inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3S1Y/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-05-16 Released: 2011-06-29 
• Deposition Author(s): Scapin, G., Lu, J., Fitzgerald, P.M.D., Sharma, N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.202 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Literature

Side chain SAR of bicyclic Beta-lactamase inhibitors (BLIs). 2. N-Alkylated and open chain analogs of MK-8712

Chen, H., Blizzard, T.A., Kim, S., Wu, J., Young, K., Park, Y.W., Ogawa, A.M., Raghoobar, S., Painter, R.E., Wisniewski, D., Hairston, N., Fitzgerald, P., Sharma, N., Scapin, G., Lu, J., Hermes, J., Hammond, M.L.

(2011) Bioorg Med Chem Lett 21: 4267-4270

• PubMed: 21676616 
• DOI: https://doi.org/10.1016/j.bmcl.2011.05.065
• Primary Citation of Related Structures:  
  3S1Y, 3S22


• PubMed Abstract: 
  

  The bridged monobactam β-lactamase inhibitor MK-8712 (1) effectively inhibits class C β-lactamases. Side chain N-alkylated and ring-opened analogs of 1 were prepared and evaluated for combination with imipenem to overcome class C β-lactamase mediated resistance. Although some analogs were more potent inhibitors of AmpC, none exhibited better synergy with imipenem than 1.

---

Organizational Affiliation: 

Departments of Medicinal Chemistry, Merck Research Labs, Rahway, NJ 07065, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.17 kDa 
• Atom Count: 3,296 
• Modelled Residue Count: 361 
• Deposited Residue Count: 371 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	371	Pseudomonas aeruginosa	Mutation(s): 1  Gene Names: ampC, PA4110 EC: 3.5.2.6
UniProt
Find proteins for P24735 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P24735  Go to UniProtKB:  P24735

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S1Y	B [auth A]	[(2S,3R)-1-{[(4S)-1-(2-aminoethyl)azepan-4-yl]carbamoyl}-2-formylpyrrolidin-3-yl]sulfamic acid C14 H27 N5 O5 S FVHVSTMGNMLCNC-YNEHKIRRSA-N
IPA	D [auth A], E [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
S1Y	PDBBind:  3S1Y	IC50: 600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.202 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.253	α = 90
b = 69.696	β = 90
c = 101.667	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
MERLOT	phasing
REFMAC	refinement
X-GEN	data reduction
X-GEN	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
Deposition Author(s): Scapin, G., Lu, J., Fitzgerald, P.M.D., Sharma, N.

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-06-26
  Changes: Database references
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary