The crystal structure of APO HUMAN HDHD4 FROM SE-MAD

Experimental Data Snapshot

  • Resolution: 1.99 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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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: https://doi.org/10.1016/j.bmcl.2013.05.052
  • Primary Citation of Related Structures:  
    4KNV, 4KNW

  • 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
241Homo sapiensMutation(s): 0 
Gene Names: C20orf147HDHD4NANP
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TBE9 (Homo sapiens)
Explore Q8TBE9 
Go to UniProtKB:  Q8TBE9
GTEx:  ENSG00000170191 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TBE9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.99 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.34α = 65.5
b = 53.436β = 74.99
c = 63.958γ = 85.17
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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