3OVN | pdb_00003ovn

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

• PDB DOI: https://doi.org/10.2210/pdb3OVN/pdb

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


• Deposited: 2010-09-16 Released: 2011-03-09 
• Deposition Author(s): Wielens, J., Chalmers, D.K., Headey, S.J., Deadman, J.J., Rhodes, D.K., Parker, M.W., Scanlon, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.249 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

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 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: 36.95 kDa 
• Atom Count: 2,286 
• Modeled Residue Count: 284 
• 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): 4  Gene Names: pol
UniProt
Find proteins for Q72498 (Human immunodeficiency virus type 1) Explore Q72498  Go to UniProtKB:  Q72498

Oligosaccharides

Help  

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPV	E [auth A], I [auth B]	1-methyl-3-(thiophen-2-yl)-1H-pyrazol-5-amine C8 H9 N3 S NFTITKUYTQZKIZ-UHFFFAOYSA-N
CD	F [auth A], G [auth A], J [auth B], K [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	D [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 1.95 Å
• R-Value Free:  0.249 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.75	α = 90
b = 59.704	β = 90
c = 81.818	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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