4IKU

Crystal structure of truncated (delta 1-89) human methionine aminopeptidase Type 1 in complex with 2-((5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl)amino)-3-phenylpropanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Identification, Biochemical and Structural Evaluation of Species-Specific Inhibitors against Type I Methionine Aminopeptidases

Kishor, C.Arya, T.Reddi, R.Chen, X.Saddanapu, V.Marapaka, A.K.Gumpena, R.Ma, D.Liu, J.O.Addlagatta, A.

(2013) J.Med.Chem. 56: 5295-5305

  • DOI: 10.1021/jm400395p
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Methionine aminopeptidases (MetAPs) are essential enzymes that make them good drug targets in cancer and microbial infections. MetAPs remove the initiator methionine from newly synthesized peptides in every living cell. MetAPs are broadly divided int ...

    Methionine aminopeptidases (MetAPs) are essential enzymes that make them good drug targets in cancer and microbial infections. MetAPs remove the initiator methionine from newly synthesized peptides in every living cell. MetAPs are broadly divided into type I and type II classes. Both prokaryotes and eukaryotes contain type I MetAPs, while eukaryotes have additional type II MetAP enzyme. Although several inhibitors have been reported against type I enzymes, subclass specificity is scarce. Here, using the fine differences in the entrance of the active sites of MetAPs from Mycobacterium tuberculosis , Enterococcus faecalis , and human, three hotspots have been identified and pyridinylpyrimidine-based molecules were selected from a commercial source to target these hotspots. In the biochemical evaluation, many of the 38 compounds displayed differential behavior against these three enzymes. Crystal structures of four selected inhibitors in complex with human MetAP1b and molecular modeling studies provided the basis for the binding specificity.


    Organizational Affiliation

    Center for Chemical Biology, CSIR-Indian Institute of Chemical Technology , Tarnaka, Hyderabad AP-500 007, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine aminopeptidase 1
A
329Homo sapiensMutation(s): 0 
Gene Names: METAP1 (KIAA0094)
EC: 3.4.11.18
Find proteins for P53582 (Homo sapiens)
Go to Gene View: METAP1
Go to UniProtKB:  P53582
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SHX
Query on SHX

Download SDF File 
Download CCD File 
A
Nalpha-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]-D-phenylalaninamide
C19 H18 Cl N5 O
SELSGPMCFPHSDG-OAHLLOKOSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SHXIC50: 1790 nM BINDINGMOAD
SHXIC50: 1790 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.493α = 90.00
b = 77.377β = 90.76
c = 48.088γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
HKL-3000data collection
HKL-3000data scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release