3AO5

Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase

• PDB DOI: https://doi.org/10.2210/pdb3AO5/pdb

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


• Deposited: 2010-09-21 Released: 2011-03-09 
• Deposition Author(s): Wielens, J., Headey, S.J., Parker, M.W., Chalmers, D.K., Scanlon, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.289 
• R-Value Work: 0.243 
• R-Value Observed: 0.246 

Starting Model: experimental

Literature

Fragment-based design of ligands targeting a novel site on the integrase enzyme of human immunodeficiency virus 1

Wielens, J., Headey, S.J., Deadman, J.J., Rhodes, D.I., Parker, M.W., Chalmers, D.K., Scanlon, M.J.

(2011) ChemMedChem 6: 258-261

• PubMed: 21275048 
• DOI: https://doi.org/10.1002/cmdc.201000483
• Primary Citation of Related Structures:  
  3AO1, 3AO2, 3AO3, 3AO4, 3AO5, 3OVN

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Organizational Affiliation: 

Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Australia.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 37.57 kDa 
• Atom Count: 2,261 
• Modelled Residue Count: 275 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POL polyprotein	A, B	163	Human immunodeficiency virus 1	Mutation(s): 7  Gene Names: POL
UniProt
Find proteins for Q72498 (Human immunodeficiency virus 1) Explore Q72498  Go to UniProtKB:  Q72498

Oligosaccharides

Help

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BBY	D [auth A], L [auth B]	5-(7-bromo-1,3-benzodioxol-5-yl)-1-methyl-1H-pyrazol-3-amine C11 H10 Br N3 O2 OZBMCGHXSVNTHG-UHFFFAOYSA-N
CD	J [auth A], K [auth A], P [auth B], Q [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	E [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
BBY	PDBBind:  3AO5	Kd: 5.90e+6 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.289 
• R-Value Work: 0.243 
• R-Value Observed: 0.246 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.032	α = 90
b = 49.032	β = 90
c = 103.724	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
AMoRE	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-09 
Deposition Author(s): Wielens, J., Headey, S.J., Parker, M.W., Chalmers, D.K., Scanlon, M.J.

Revision History  

• Version 1.0: 2011-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary