Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 80.71 kDa 
• Atom Count: 6182 
• Modelled Residue Count: 716 
• Deposited Residue Count: 716 
• Unique protein chains: 1

2HDQ

AmpC beta-lactamase in complex with 2-carboxythiophene

• DOI: 10.2210/pdb2HDQ/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-06-20 Released: 2006-11-07 
• Deposition Author(s): Babaoglu, K., Shoichet, B.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.227 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 

Literature

Deconstructing fragment-based inhibitor discovery

Babaoglu, K., Shoichet, B.K.

(2006) Nat Chem Biol 2: 720-723

• PubMed: 17072304 
• DOI: 10.1038/nchembio831
• Primary Citation of Related Structures:  
  2HDU, 2HDS, 2HDR, 2HDQ


• PubMed Abstract: 
  

Fragment-based screens test multiple low-molecular weight molecules for binding to a target. Fragments often bind with low affinities but typically have better ligand efficiencies (DeltaG(bind)/heavy atom count) than traditional screening hits. This efficiency, combined with accompanying atomic-resolution structures, has made fragments popular starting points for drug discovery programs. Fragment-based design adopts a constructive strategy: affinity is enhanced either by cycles of functional-group addition or by joining two independent fragments together. The final inhibitor is expected to adopt the same geometry as the original fragment hit. Here we consider whether the inverse, deconstructive logic also applies--can one always parse a higher-affinity inhibitor into fragments that recapitulate the binding geometry of the larger molecule? Cocrystal structures of fragments deconstructed from a known beta-lactamase inhibitor suggest that this is not always the case.

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Organizational Affiliation: 

Abteilung für Strukturforschung, Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, Martinsried, D-82152, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	358	Escherichia coli K-12	Mutation(s): 0  Gene Names: ampC, ampA, b4150, JW4111 EC: 3.5.2.6
Find proteins for P00811 (Escherichia coli (strain K12)) Explore P00811  Go to UniProtKB:  P00811

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C21	A, B	THIOPHENE-2-CARBOXYLIC ACID C5 H4 O2 S QERYCTSHXKAMIS-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
C21	Ki :  40000000   nM  PDBBind
C21	Ki:  40000000   nM  BindingDB
C21	Ki:  40000000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.227 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.434	α = 90
b = 74.781	β = 116.14
c = 98.281	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-06-20 
• Released Date: 2006-11-07 
Deposition Author(s): Babaoglu, K., Shoichet, B.K.

Revision History  

• Version 1.0: 2006-11-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance