2G70

Structure of human PNMT in complex with inhibitor 3-hydroxymethyl-7-nitro-THIQ and AdoMet (SAM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Enzyme Adaptation to Inhibitor Binding: A Cryptic Binding Site in Phenylethanolamine N-Methyltransferase

Gee, C.L.Drinkwater, N.Tyndall, J.D.A.Grunewald, G.L.Wu, Q.McLeish, M.J.Martin, J.L.

(2007) J.Med.Chem. 50: 4845-4853

  • DOI: 10.1021/jm0703385
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Shape complementarity is a fundamental principle of inhibitor design. Here we show that an enzyme for which the crystal structure has been determined (phenylethanolamine N-methyltransferase, PNMT) conceals a cryptic binding site. This site is reveale ...

    Shape complementarity is a fundamental principle of inhibitor design. Here we show that an enzyme for which the crystal structure has been determined (phenylethanolamine N-methyltransferase, PNMT) conceals a cryptic binding site. This site is revealed upon binding of inhibitors that are double the size of the physiological substrate. These large inhibitors are not predicted to bind in that they protrude through the accessible surface calculated from a PNMT/7-aminosulfonyl-1,2,3,4-tetrahydroisoquinoline (SK&F 29661) crystal structure, yet they are potent inhibitors of PNMT. We determined structures of the enzyme complexed with large inhibitors and found that the volume of the active site increases by 140 A3 upon binding. Changes in active site size and shape are brought about by unfavorable side chain conformations and rigid body helix motions. The energetic cost is modest, estimated at 2-3 kcal/mol from mutational analyses. Our findings further underline the importance of protein flexibility in structure-based inhibitor design studies.


    Organizational Affiliation

    Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, University of Queensland, Brisbane, Qld, 4072 Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenylethanolamine N-methyltransferase
A, B
289Homo sapiensMutation(s): 0 
Gene Names: PNMT (PENT)
EC: 2.1.1.28
Find proteins for P11086 (Homo sapiens)
Go to Gene View: PNMT
Go to UniProtKB:  P11086
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HNT
Query on HNT

Download SDF File 
Download CCD File 
A, B
[(3R)-7-NITRO-1,2,3,4-TETRAHYDROISOQUINOLIN-3-YL]METHANOL
3(R)-HYDROXYMETHYL 7-NITRO 1,2,3,4-TETRAHYDROISOQUINOLINE
C10 H12 N2 O3
RNUCRXHRBPLYTA-SECBINFHSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HNTKi: 17 - 47 nM (100) BINDINGDB
HNTKi: 17 nM BINDINGMOAD
HNTKi: 17 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.240 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.240α = 90.00
b = 94.240β = 90.00
c = 187.810γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
CNSphasing
PDB_EXTRACTdata extraction
CNSrefinement
d*TREKdata processing
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2007-10-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance