3QIP

Structure of HIV-1 reverse transcriptase in complex with an RNase H inhibitor and nevirapine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0926 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Binding Analysis of Pyrimidinol Carboxylic Acid and N-Hydroxy Quinazolinedione HIV-1 RNase H Inhibitors.

Lansdon, E.B.Liu, Q.Leavitt, S.A.Balakrishnan, M.Perry, J.K.Lancaster-Moyer, C.Kutty, N.Liu, X.Squires, N.H.Watkins, W.J.Kirschberg, T.A.

(2011) Antimicrob.Agents Chemother. 55: 2905-2915

  • DOI: 10.1128/AAC.01594-10
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HIV-1 RNase H breaks down the intermediate RNA-DNA hybrids during reverse transcription, requiring two divalent metal ions for activity. Pyrimidinol carboxylic acid and N-hydroxy quinazolinedione inhibitors were designed to coordinate the two metal i ...

    HIV-1 RNase H breaks down the intermediate RNA-DNA hybrids during reverse transcription, requiring two divalent metal ions for activity. Pyrimidinol carboxylic acid and N-hydroxy quinazolinedione inhibitors were designed to coordinate the two metal ions in the active site of RNase H. High-resolution (1.4 Å to 2.1 Å) crystal structures were determined with the isolated RNase H domain and reverse transcriptase (RT), which permit accurate assessment of the metal and water environment at the active site. The geometry of the metal coordination suggests that the inhibitors mimic a substrate state prior to phosphodiester catalysis. Surface plasmon resonance studies confirm metal-dependent binding to RNase H and demonstrate that the inhibitors do not bind at the polymerase active site of RT. Additional evaluation of the RNase H site reveals an open protein surface with few additional interactions to optimize active-site inhibitors.


    Organizational Affiliation

    Gilead Sciences, Inc., 333 Lakeside Dr., Foster City, CA 94404, USA. eric.lansdon@gilead.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse HIV-1 reverse transcriptase p66
A
560Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
p51
B
440Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NVP
Query on NVP

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Download CCD File 
A
11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE
NON-NUCLEOSIDE RT INHIBITOR NEVIRAPINE
C15 H14 N4 O
NQDJXKOVJZTUJA-UHFFFAOYSA-N
 Ligand Interaction
P4Y
Query on P4Y

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Download CCD File 
A
5,6-dihydroxy-2-[(2-phenyl-1H-indol-3-yl)methyl]pyrimidine-4-carboxylic acid
C20 H15 N3 O4
JONQCFJPPWOWOJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P4YKd: 129 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0926 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.216 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 118.898α = 90.00
b = 154.876β = 90.00
c = 153.079γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
BOSdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance