3HYF

Crystal structure of HIV-1 RNase H p15 with engineered E. coli loop and active site inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

RNase H active site inhibitors of human immunodeficiency virus type 1 reverse transcriptase: design, biochemical activity, and structural information.

Kirschberg, T.A.Balakrishnan, M.Squires, N.H.Barnes, T.Brendza, K.M.Chen, X.Eisenberg, E.J.Jin, W.Kutty, N.Leavitt, S.Liclican, A.Liu, Q.Liu, X.Mak, J.Perry, J.K.Wang, M.Watkins, W.J.Lansdon, E.B.

(2009) J.Med.Chem. 52: 5781-5784

  • DOI: 10.1021/jm900597q

  • PubMed Abstract: 
  • Pyrimidinol carboxylic acids were designed as inhibitors of HIV-1 RNase H function. These molecules can coordinate to two divalent metal ions in the RNase H active site. Inhibition of enzymatic activity was measured in a biochemical assay, but no ant ...

    Pyrimidinol carboxylic acids were designed as inhibitors of HIV-1 RNase H function. These molecules can coordinate to two divalent metal ions in the RNase H active site. Inhibition of enzymatic activity was measured in a biochemical assay, but no antiviral effect was observed. Binding was demonstrated via a solid state structure of the isolated p15-Ec domain of HIV-1 RT showing inhibitor and two Mn(II) ions bound to the RNase H active site.


    Organizational Affiliation

    Department of Medicinal Chemistry, Gilead Sciences, Foster City, California 94404, USA. tkirschberg@gilead.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/RNaseH
A
150Escherichia coli (strain K12)Human immunodeficiency virus 1
This entity is chimeric
Mutation(s): 0 
Gene Names: rnhA (dasF, herA, rnh, sdrA), pol
EC: 3.1.26.4
Find proteins for P0A7Y4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Y4
Find proteins for Q72547 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q72547
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ON1
Query on ON1

Download SDF File 
Download CCD File 
A
2-(3,4-dichlorobenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid
C12 H8 Cl2 N2 O4
OZDSTVKQUHMIRA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ON1IC50: 1450 nM (84) BINDINGDB
ON1IC50: 1200 nM BINDINGMOAD
ON1IC50: 1200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.717α = 90.00
b = 90.326β = 90.00
c = 113.334γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data scaling
HKL-2000data reduction
CNXrefinement
BOSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2011-11-16
    Type: Atomic model
  • Version 1.3: 2017-08-16
    Type: Refinement description, Source and taxonomy