Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 115398.26 
• Atom Count: 8072 
• Residue Count: 981 
• Unique protein chains: 2

2I5J

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with DHBNH, an RNASE H inhibitor

• DOI: 10.2210/pdb2I5J/pdb

• Classification: TRANSFERASE
• Organism(s): Human immunodeficiency virus 1, Human immunodeficiency virus type 1 group M subtype B
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2006-08-24 Released: 2006-12-05 
• Deposition Author(s): Himmel, D.M., Sarafianos, S.G., Knight, J.L., Levy, R.M., Arnold, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.269 
• R-Value Work: 0.234 

Literature

HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site.

Himmel, D.M., Sarafianos, S.G., Dharmasena, S., Hossain, M.M., McCoy-Simandle, K., Ilina, T., Clark, A.D., Knight, J.L., Julias, J.G., Clark, P.K., Krogh-Jespersen, K., Levy, R.M., Hughes, S.H., Parniak, M.A., Arnold, E.

(2006) Acs Chem.Biol. 1: 702-712

• PubMed: 17184135 
• DOI: 10.1021/cb600303y


• PubMed Abstract: 
  

The rapid emergence of drug-resistant variants of human immunodeficiency virus, type 1 (HIV-1), has limited the efficacy of anti-acquired immune deficiency syndrome (AIDS) treatments, and new lead compounds that target novel binding sites are needed. We have determined the 3.15 A resolution crystal structure of HIV-1 reverse transcriptase (RT) complexed with dihydroxy benzoyl naphthyl hydrazone (DHBNH), an HIV-1 RT RNase H (RNH) inhibitor (RNHI). DHBNH is effective against a variety of drug-resistant HIV-1 RT mutants. While DHBNH has little effect on most aspects of RT-catalyzed DNA synthesis, at relatively high concentrations it does inhibit the initiation of RNA-primed DNA synthesis. Although primarily an RNHI, DHBNH binds >50 A away from the RNH active site, at a novel site near both the polymerase active site and the non-nucleoside RT inhibitor (NNRTI) binding pocket. When DHBNH binds, both Tyr181 and Tyr188 remain in the conformations seen in unliganded HIV-1 RT. DHBNH interacts with conserved residues (Asp186, Trp229) and has substantial interactions with the backbones of several less well-conserved residues. On the basis of this structure, we designed substituted DHBNH derivatives that interact with the NNRTI-binding pocket. These compounds inhibit both the polymerase and RNH activities of RT.

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Related Citations: 

• Crystal Structures for HIV-1 Reverse Transcriptase in Complexes with Three Pyridinone Derivatives: A New Class of Non-nucleoside Inhibitors Effective Against a Broad Range of Drug-Resistant Strains
  Himmel, D.M.,Das, K.,Clark Jr., A.D.,Hughes, S.H.,Benjahad, A.,Oumouch, S.,Guillemont, J.,Coupa, S.,Poncelet, A.,Csoka, I.,Meyer, C.,Andries, K.,Nguyen, C.H.,Grierson, D.S.,Arnold, E.
  (2005) J.Med.Chem. 48: 7582
• Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA
  Sarafianos, S.G.,Das, K.,Tantillo, C.,Clark Jr., A.D.,Ding, J.,Whitcomb, J.M.,Boyer, P.L.,Hughes, S.H.,Arnold, E.
  (2001) EMBO J. 20: 1449
• Structure and Functional Implications of the Polymerase Active Site Region in a Complex of HIV-1 RT with a Double-Stranded DNA Template-Primer and an Antibody Fab Fragment at 2.8 A Resolution.
  Ding, J.,Das, K.,Hsiou, Y.,Sarafianos, S.G.,Clark Jr., A.D.,Jacobo-Molina, A.,Tantillo, C.,Hughes, S.H.,Arnold, E.
  (1998) J.Mol.Biol. 284: 1095
• Structure of unliganded HIV-1 reverse transcriptase t 2.7 A resolution: implications of conformational hanges for polymerization and inhibition mechanisms
  Hsiou, Y.,Ding, J.,Das, K.,Clark Jr., A.D.,Hughes, S.H.,Arnold, E.
  (1996) Structure 4: 853
• Roles of Conformational and Positional Adaptability in Structure-Based Design of Tmc125-R165335 (Etravirine) and Related Non-Nucleoside Reverse Transcriptase Inhibitors that are Highly Potent and Effective Against Wild-Type and Drug-Resistant HIV-1 Variants
  Das, K.,Clark Jr., A.D.,Lewi, P.J.,Heeres, J.,De Jonge, M.R.,Koymans, L.M.H.,Vinkers, H.M.,Daeyaert, F.,Ludovici, D.W.,Kukla, M.J.,De Corte, B.,Kavash, R.W.,Ho, C.Y.,Ye, H.,Lichtenstein, M.A.,Andries, K.,Pauwels, R.,De Bethune, M.-P.,Boyer, P.L.,Clark, P.,Hughes, S.H.,Janssen, P.A.J.,Arnold, E.
  (2004) J.Med.Chem. 47: 2550




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Organizational Affiliation: 

Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-5627, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Reverse transcriptase/ribonuclease H P66 subunit	A	552	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 1  Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P03366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Reverse transcriptase/ribonuclease H P51 subunit	B	429	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: pol
Find proteins for Q8UM83 (Human immunodeficiency virus 1) Go to UniProtKB:  Q8UM83

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SUC	A, B	SUCROSE C12 H22 O11 CZMRCDWAGMRECN-UGDNZRGBSA-N
GLC	A, B	ALPHA-D-GLUCOSE C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
K05	A	(E)-3,4-DIHYDROXY-N'-[(2-METHOXYNAPHTHALEN-1-YL)METHYLENE]BENZOHYDRAZIDE C19 H16 N2 O4 TVOPERZEGKBKAY-RGVLZGJSSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
K05	IC50: 500 - >25000 nM (100) BINDINGDB
K05	IC50: 500 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.269 
• R-Value Work: 0.234 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 224.815	α = 90.00
b = 68.896	β = 106.48
c = 104.662	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
DENZO	data reduction
HKL-2000	data collection
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-08-24 
• Released Date: 2006-12-05 
• Deposition Author(s): Himmel, D.M., Sarafianos, S.G., Knight, J.L., Levy, R.M., Arnold, E.

Revision History 

• Version 1.0: 2006-12-05
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-18
  Type: Refinement description