4IKR

Crystal structure of Type 1 human methionine aminopeptidase in complex with 2-(4-(5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl)piperazin-1-yl)ethanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


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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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PVP
Query on PVP

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Download CCD File 
A
2-{4-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]piperazin-1-yl}ethanol
C16 H20 Cl N5 O
NLGYGVCRRXIJRR-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

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Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PVPIC50: 1100 nM (100) BINDINGDB
PVPIC50: 590 nM BINDINGMOAD
PVPIC50: 590 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.345α = 90.00
b = 77.423β = 91.03
c = 48.023γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
HKL-3000data collection
REFMACrefinement
HKL-3000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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