1THZ

Crystal Structure of Avian AICAR Transformylase in Complex with a Novel Inhibitor Identified by Virtual Ligand Screening


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of avian aminoimidazole-4-carboxamide ribonucleotide transformylase in complex with a novel non-folate inhibitor identified by virtual ligand screening.

Xu, L.Li, C.Olson, A.J.Wilson, I.A.

(2004) J Biol Chem 279: 50555-50565

  • DOI: 10.1074/jbc.M406801200
  • Primary Citation of Related Structures:  
    1THZ

  • PubMed Abstract: 
  • Aminoimidazole-4-carboxamide ribonucleotide transformylase (AICAR Tfase), one of the two folate-dependent enzymes in the de novo purine biosynthesis pathway, is a promising target for anti-neoplastic chemotherapy. Although classic antifolates, such as methotrexate, have been developed as anticancer agents, their general toxicity and drug resistance are major issues associated with their clinical use and future development ...

    Aminoimidazole-4-carboxamide ribonucleotide transformylase (AICAR Tfase), one of the two folate-dependent enzymes in the de novo purine biosynthesis pathway, is a promising target for anti-neoplastic chemotherapy. Although classic antifolates, such as methotrexate, have been developed as anticancer agents, their general toxicity and drug resistance are major issues associated with their clinical use and future development. Identification of inhibitors with novel scaffolds could be an attractive alternative. We present here the crystal structure of avian AICAR Tfase complexed with the first non-folate based inhibitor identified through virtual ligand screening of the National Cancer Institute Diversity Set. The inhibitor 326203-A (2-[5-hydroxy-3-methyl-1-(2-methyl-4-sulfophenyl)-1H-pyrazol-4-ylazo]-4-sulfo-benzoic acid) displayed competitive inhibition against the natural cofactor, 10-formyl-tetrahydrofolate, with a K(i) of 7.1 mum. The crystal structure of AICAR Tfase with 326203-A at 1.8 A resolution revealed a unique binding mode compared with antifolate inhibitors. The inhibitor also accessed an additional binding pocket that is not occupied by antifolates. The sulfonate group of 326203-A appears to form the dominant interaction of the inhibitor with the proposed oxyanion hole through interaction with a helix dipole and Lys(267). An aromatic interaction with Phe(316) also likely contributes to favorable binding. Based on these structural insights, several inhibitors with improved potency were subsequently identified in the National Cancer Institute Compound Library and the Available Chemical Directory by similarity search and molecular modeling methods. These results provide further support for our combined virtual ligand screening rational design approach for the discovery of novel, non-folate-based inhibitors of AICAR Tfase.


    Related Citations: 
    • Structural Insights Into the Avian Aicar Transformylase Mechanism
      Wolan, D.W., Greasley, S.E., Bearsley, G.P., Wilson, I.A.
      (2002) Biochemistry 41: 15505
    • Structure of Avian Aicar Transformylase with a Multisubstrate Adduct Inhibitor Beta-Dadf Identifies the Folate Binding Site
      Wolan, D.W., Greasley, S.E., Wall, M.J., Benkovic, S.J., Wilson, I.A.
      (2003) Biochemistry 42: 10904
    • Structural Insights Into the Human and Avian Imp Cyclohydrolase Mechanism Via Crystal Structures with the Bound Xmp Inhibitor
      Wolan, D.W., Cheong, C.G., Greasley, S.E., Wilson, I.A.
      (2004) Biochemistry 43: 1171
    • Crystal structures of human bifunctional enzyme aminoimidazole-4-carboxamide ribonucleotide transformylase/IMP cyclohydrolase in complex with potent sulfonyl-containing antifolates.
      Cheong, C.G., Woland, D.W., Greasley, S.E., Horton, P.A., Beardsley, G.P., Wilson, I.A.
      (2004) J Biol Chem 279: 18034
    • Crystal structure of a bifunctional transformylase and cyclohydrolase enzyme in purine biosynthesis.
      Greasley, S.E., Horton, P.A., Ramcharan, J., Bearsley, G.P., Benkovic, S.J., Wilson, I.A.
      (2001) Nat Struct Mol Biol 8: 402

    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional purine biosynthesis protein PURH AB593Gallus gallusMutation(s): 0 
Gene Names: ATICPURH
EC: 2.1.2.3 (PDB Primary Data), 3.5.4.10 (PDB Primary Data)
Find proteins for P31335 (Gallus gallus)
Explore P31335 
Go to UniProtKB:  P31335
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
326
Query on 326

Download Ideal Coordinates CCD File 
A, B
2-{(E)-[5-HYDROXY-3-METHYL-1-(2-METHYL-4-SULFOPHENYL)-1H-PYRAZOL-4-YL]DIAZENYL}-4-SULFOBENZOIC ACID
C18 H16 N4 O9 S2
NOQURKNIKJDEPW-FMQUCBEESA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
326Ki:  7100   nM  Binding MOAD
326Ki :  7100   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.8α = 90
b = 105.3β = 108.1
c = 102.4γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance