4IU6 | pdb_00004iu6

Human Methionine Aminopeptidase in complex with FZ1: Pyridinylquinazolines Selectively Inhibit Human Methionine Aminopeptidase-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.223 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Pyridinylquinazolines selectively inhibit human methionine aminopeptidase-1 in cells.

Zhang, F.Bhat, S.Gabelli, S.B.Chen, X.Miller, M.S.Nacev, B.A.Cheng, Y.L.Meyers, D.J.Tenney, K.Shim, J.S.Crews, P.Amzel, L.M.Ma, D.Liu, J.O.

(2013) J Med Chem 56: 3996-4016

  • DOI: https://doi.org/10.1021/jm400227z
  • Primary Citation Related Structures: 
    4IU6

  • PubMed Abstract: 

    Methionine aminopeptidases (MetAPs), which remove the initiator methionine from nascent peptides, are essential in all organisms. While MetAP2 has been demonstrated to be a therapeutic target for inhibiting angiogenesis in mammals, MetAP1 seems to be vital for cell proliferation. Our earlier efforts identified two structural classes of human MetAP1 (HsMetAP1)-selective inhibitors (1-4), but all of them failed to inhibit cellular HsMetAP1. Using Mn(II) or Zn(II) to activate HsMetAP1, we found that 1-4 could only effectively inhibit purified HsMetAP1 in the presence of physiologically unachievable concentrations of Co(II). In an effort to seek Co(II)-independent inhibitors, a novel structural class containing a 2-(pyridin-2-yl)quinazoline core has been discovered. Many compounds in this class potently and selectively inhibited HsMetAP1 without Co(II). Subsequently, we demonstrated that 11j, an auxiliary metal-dependent inhibitor, effectively inhibited HsMetAP1 in primary cells. This is the first report that an HsMetAP1-selective inhibitor is effective against its target in cells.


  • Organizational Affiliation
    • Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.

Macromolecule Content 

  • Total Structure Weight: 43.81 kDa 
  • Atom Count: 2,731 
  • Modeled Residue Count: 304 
  • Deposited Residue Count: 384 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methionine aminopeptidase 1384Homo sapiensMutation(s): 0 
Gene Names: METAP1KIAA0094
EC: 3.4.11.18
UniProt & NIH Common Fund Data Resources
Find proteins for P53582 (Homo sapiens)
Explore P53582 
Go to UniProtKB:  P53582
PHAROS:  P53582
GTEx:  ENSG00000164024 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53582
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FZ1

Query on FZ1



Download:Ideal Coordinates CCD File
F [auth A]4-[4-(4-methoxyphenyl)piperazin-1-yl]-2-(pyridin-2-yl)quinazoline
C24 H23 N5 O
BNLATJNUBANGFF-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CO

Query on CO



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
E [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.223 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.303α = 90
b = 77.344β = 91.49
c = 47.821γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-05-15
    Changes: Database references
  • Version 1.2: 2013-11-27
    Changes: Database references
  • Version 1.3: 2019-11-20
    Changes: Derived calculations
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations