4KNW

The crystal structure of human HDHD4 IN COMPLEX WITH MAGNESIUM AND THE PHOSPHATE MIMETIC VANADATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.699 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design, synthesis, functional and structural characterization of an inhibitor of N-acetylneuraminate-9-phosphate phosphatase: Observation of extensive dynamics in an enzyme/inhibitor complex.

Kim, S.H.Constantine, K.L.Duke, G.J.Goldfarb, V.Hunt, J.T.Johnson, S.Kish, K.Klei, H.E.McDonnell, P.A.Metzler, W.J.Mueller, L.Poss, M.A.Fairchild, C.R.Bhide, R.S.

(2013) Bioorg.Med.Chem.Lett. 23: 4107-4111

  • DOI: 10.1016/j.bmcl.2013.05.052
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The design, synthesis and characterization of a phosphonate inhibitor of N-acetylneuraminate-9-phosphate phosphatase (HDHD4) is described. Compound 3, where the substrate C-9 oxygen was replaced with a nonlabile CH2 group, inhibits HDHD4 with a bindi ...

    The design, synthesis and characterization of a phosphonate inhibitor of N-acetylneuraminate-9-phosphate phosphatase (HDHD4) is described. Compound 3, where the substrate C-9 oxygen was replaced with a nonlabile CH2 group, inhibits HDHD4 with a binding affinity (IC50 11μM) in the range of the native substrate Neu5Ac-9-P (compound 1, Km 47μM). Combined SAR, modeling and NMR studies are consistent with the phosphonate group in inhibitor 3 forming a stable complex with native Mg(2+). In addition to this key interaction, the C-1 carboxylate of the sugar interacts with a cluster of basic residues, K141, R104 and R72. Comparative NMR studies of compounds 3 and 1 with Ca(2+) and Mg(2+) are indicative of a highly dynamic process in the active site for the HDHD4/Mg(2+)/3 complex. Possible explanations for this observation are discussed.


    Organizational Affiliation

    Bristol-Myers Squibb Research and Development, 311 Pennington-Rocky Hill Road, Pennington, NJ 08534, USA. soonghoon.kim@bms.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acylneuraminate-9-phosphatase
A, B, C
257Homo sapiensMutation(s): 0 
Gene Names: NANP (C20orf147, HDHD4)
EC: 3.1.3.29
Find proteins for Q8TBE9 (Homo sapiens)
Go to Gene View: NANP
Go to UniProtKB:  Q8TBE9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
VO4
Query on VO4

Download SDF File 
Download CCD File 
A, B, C
VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.699 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.254 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.777α = 90.00
b = 102.560β = 90.00
c = 186.665γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data reduction
CNSrefinement
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-05-10 
  • Released Date: 2013-06-26 
  • Deposition Author(s): Klei, H.E.

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references