2GG9

Novel bacterial methionine aminopeptidase inhibitors

• PDB DOI: https://doi.org/10.2210/pdb2GG9/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-03-23 Released: 2006-06-13 
• Deposition Author(s): Evdokimov, A.G., Pokross, M.E., Walter, R.L., Mekel, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.159 
• R-Value Work: 0.140 
• R-Value Observed: 0.140 

Starting Model: experimental

Literature

Serendipitous discovery of novel bacterial methionine aminopeptidase inhibitors.

Evdokimov, A.G., Pokross, M., Walter, R.L., Mekel, M., Barnett, B.L., Amburgey, J., Seibel, W.L., Soper, S.J., Djung, J.F., Fairweather, N., Diven, C., Rastogi, V., Grinius, L., Klanke, C., Siehnel, R., Twinem, T., Andrews, R., Curnow, A.

(2007) Proteins 66: 538-546

• PubMed: 17120228 
• DOI: https://doi.org/10.1002/prot.21207
• Primary Citation of Related Structures:  
  2GG0, 2GG2, 2GG3, 2GG5, 2GG7, 2GG8, 2GG9, 2GGB, 2GGC


• PubMed Abstract: 
  

  In this article we describe the application of structural biology methods to the discovery of novel potent inhibitors of methionine aminopeptidases. These enzymes are employed by the cells to cleave the N-terminal methionine from nascent peptides and proteins. As this is one of the critical steps in protein maturation, it is very likely that inhibitors of these enzymes may prove useful as novel antibacterial agents. Involvement of crystallography at the very early stages of the inhibitor design process resulted in serendipitous discovery of a new inhibitor class, the pyrazole-diamines. Atomic-resolution structures of several inhibitors bound to the enzyme illuminate a new mode of inhibitor binding.

---

Organizational Affiliation: 

Structural Biology Core Facility, The Procter & Gamble Pharmaceuticals, Mason, Ohio 45040, 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: 29.8 kDa 
• Atom Count: 2,588 
• Modelled Residue Count: 263 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase	A	263	Escherichia coli K-12	Mutation(s): 0  Gene Names: map EC: 3.4.11.18
UniProt
Find proteins for P0AE18 (Escherichia coli (strain K12)) Explore P0AE18  Go to UniProtKB:  P0AE18

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U16	E [auth A]	METHYL N-[(2S,3R)-3-AMINO-2-HYDROXY-3-(4-ISOPROPYLPHENYL)PROPANOYL]-D-ALANYL-D-LEUCINATE C22 H35 N3 O5 WIWZNHHLFMPGGO-PIKADFDJSA-N
CO	B [auth A], C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
U16	PDBBind:  2GG9	IC50: 3500 (nM) from 1 assay(s)
	BindingDB:  2GG9	IC50: 3500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.159 
• R-Value Work: 0.140 
• R-Value Observed: 0.140 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.131	α = 90
b = 63.29	β = 109.71
c = 52.513	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-13 
Deposition Author(s): Evdokimov, A.G., Pokross, M.E., Walter, R.L., Mekel, M.

Revision History  

• Version 1.0: 2006-06-13
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description