3OVN

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.249
R-Value Work: 0.211
R-Value Observed: 0.213

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 36.95 kDa
Atom Count: 2,286
Modelled Residue Count: 284
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q72498
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPV Query on MPV Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	1-methyl-3-(thiophen-2-yl)-1H-pyrazol-5-amine C₈ H₉ N₃ S NFTITKUYTQZKIZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	F [auth A], G [auth A], J [auth B], K [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
MPV	PDBBind: 3OVN	Kd: 2.80e+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 Query on PRD_900003	C	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.249
R-Value Work: 0.211
R-Value Observed: 0.213
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-03-09

Deposition Author(s):

Revision History (Full details and data files)

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

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Help and Resources

3OVN

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2