1Y2F | pdb_00001y2f

Crystal Structure of ZipA with an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1Y2F/pdb

• Classification: CELL CYCLE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2004-11-22 Released: 2005-03-01 
• Deposition Author(s): Mosyak, L., Rush, T.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.228 (Depositor) 
• R-Value Work: 
  0.225 (Depositor) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction

Rush, T.S., Grant, J.A., Mosyak, L., Nicholls, A.

(2005) J Med Chem 48: 1489-1495

• PubMed: 15743191 
• DOI: https://doi.org/10.1021/jm040163o
• Primary Citation Related Structures: 
  1Y2F, 1Y2G


• PubMed Abstract: 
  

  In this paper, we describe the first prospective application of the shape-comparison program ROCS (Rapid Overlay of Chemical Structures) to find new scaffolds for small molecule inhibitors of the ZipA-FtsZ protein-protein interaction, a proposed antibacterial target. The shape comparisons are made relative to the crystallographically determined, bioactive conformation of a high-throughput screening (HTS) hit. The use of ROCS led to the identification of a set of novel, weakly binding inhibitors with scaffolds presenting synthetic opportunities to further optimize biological affinity and lacking development issues associated with the HTS lead. These ROCS-identified scaffolds would have been missed using other structural similarity approaches such as ISIS 2D fingerprints. X-ray crystallographic analysis of one of the new inhibitors bound to ZipA reveals that the shape comparison approach very accurately predicted the binding mode. These experimental results validate this use of ROCS for chemotype switching or "lead hopping" and suggest that it is of general interest for lead identification in drug discovery endeavors.

---

Organizational Affiliation: 
• Department of Chemical & Screening Sciences, Wyeth Research, 87 Cambridge Park Drive, Cambridge, MA 02140, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.96 kDa 
• Atom Count: 1,341 
• Modeled Residue Count: 139 
• Deposited Residue Count: 139 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein zipA	A	139	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P77173 (Escherichia coli (strain K12)) Explore P77173  Go to UniProtKB:  P77173

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WAI	B [auth A]	4-{2-[4-(2-AMINOETHYL)PIPERAZIN-1-YL]PYRIDIN-4-YL}-N-(3-CHLORO-4-METHYLPHENYL)PYRIMIDIN-2-AMINE C22 H26 Cl N7 RHOOHUMOHVIXEF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.228 (Depositor) 
• R-Value Work:  0.225 (Depositor) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.973	α = 90
b = 50.614	β = 90
c = 84.399	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-01 
Deposition Author(s): Mosyak, L., Rush, T.S.

Revision History  

• Version 1.0: 2005-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description