Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 115.40 kDa 
• Atom Count: 8108 
• Modelled Residue Count: 972 
• Deposited Residue Count: 981 
• Unique protein chains: 2

2I5J

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

• PDB DOI: 10.2210/pdb2I5J/pdb

• Classification: TRANSFERASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.269 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 

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
• Primary Citation of Related Structures:  
  2I5J


• 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.

---

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

• 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

• 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

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H P66 subunit	A	552	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: gag EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H P51 subunit	B	429	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: gag, pol EC: 2.7.7.49
UniProt
Find proteins for Q8UM83 (Human immunodeficiency virus 1) Explore Q8UM83  Go to UniProtKB:  Q8UM83

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K05	G [auth A]	(E)-3,4-DIHYDROXY-N'-[(2-METHOXYNAPHTHALEN-1-YL)METHYLENE]BENZOHYDRAZIDE C19 H16 N2 O4 TVOPERZEGKBKAY-RGVLZGJSSA-N
GLC	E [auth A], F [auth A], I [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
MG	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
K05	BindingDB:  2I5J	IC50: min: 500, max: 2.50e+4 (nM) from 8 assay(s)
	PDBBind:  2I5J	IC50: 500 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C, D	sucrose	Oligosaccharide / Nutrient		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.269 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.815	α = 90
b = 68.896	β = 106.48
c = 104.662	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary