4U73

HsMetAP(F309M) IN COMPLEX WITH (amino(phenyl)methyl)phosphonic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of the Molecular Basis of Inhibitor Selectivity between the Human and Streptococcal Type I Methionine Aminopeptidases

Arya, T.Reddi, R.Kishor, C.Ganji, R.J.Bhukya, S.Gumpena, R.McGowan, S.Drag, M.Addlagatta, A.

(2015) J Med Chem 58: 2350-2357

  • DOI: 10.1021/jm501790e
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The methionine aminopeptidase (MetAP) family is responsible for the cleavage of the initiator methionine from newly synthesized proteins. Currently, there are no small molecule inhibitors that show selectivity toward the bacterial MetAPs compared to ...

    The methionine aminopeptidase (MetAP) family is responsible for the cleavage of the initiator methionine from newly synthesized proteins. Currently, there are no small molecule inhibitors that show selectivity toward the bacterial MetAPs compared to the human enzyme. In our current study, we have screened 20 α-aminophosphonate derivatives and identified a molecule (compound 15) that selectively inhibits the S. pneumonia MetAP in low micromolar range but not the human enzyme. Further bioinformatics, biochemical, and structural analyses suggested that phenylalanine (F309) in the human enzyme and methionine (M205) in the S. pneumonia MetAP at the analogous position render them with different susceptibilities against the identified inhibitor. X-ray crystal structures of various inhibitors in complex with wild type and F309M enzyme further established the molecular basis for the inhibitor selectivity.


    Organizational Affiliation

    Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology , Hyderabad 500 007, India.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine aminopeptidase 1
A
306Homo sapiensMutation(s): 1 
Gene Names: METAP1KIAA0094
EC: 3.4.11.18
Find proteins for P53582 (Homo sapiens)
Go to UniProtKB:  P53582
NIH Common Fund Data Resources
PHAROS  P53582
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Q02
Query on Q02

Download CCD File 
A
[(R)-amino(phenyl)methyl]phosphonic acid
C7 H10 N O3 P
ZKFNOUUKULVDOB-SSDOTTSWSA-N
 Ligand Interaction
CO
Query on CO

Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Q02Ki:  111600   nM  BindingDB
Q02Ki:  6600   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.477α = 90
b = 77.296β = 91.19
c = 48.271γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references, Derived calculations, Source and taxonomy