7RQ0 | pdb_00007rq0

HIV Integrase CORE domain in complex with 2-{2-[2-(3-{[4-(2-{[(3-{2-[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}phenyl)methyl]amino}ethyl)piperazin-1-yl]methyl}phenyl)ethynyl]-5-methyl-1-benzofuran-3-yl}acetic acid

PDB DOI: https://doi.org/10.2210/pdb7RQ0/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-08-05 Released: 2022-08-10
Deposition Author(s): Gorman, M.A., Parker, M.W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.270 (Depositor), 0.242 (DCC)
R-Value Work:
0.230 (Depositor), 0.242 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

HIV integrase-LEDGF interaction screening by fragment linking using off-rate screening

Gorman, M.A., Parker, M.W.

To be published.

Macromolecule Content

Total Structure Weight: 37.63 kDa
Atom Count: 2,280
Modeled Residue Count: 276
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A, B	163	Human immunodeficiency virus 1	Mutation(s): 0 EC: 2.7.7
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497 Go to UniProtKB: P12497
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12497
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6I2 (Subject of Investigation/LOI) Query on 6I2 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	{2-[(3-{[4-(2-{[(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}phenyl)methyl]amino}ethyl)piperazin-1-yl]methyl}phenyl)ethynyl]-5-methyl-1-benzofuran-3-yl}acetic acid C₄₆ H₄₃ N₃ O₆ PQJUNYNNRHSPEP-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	E [auth A], F [auth A], G [auth A], M [auth B], N [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] H [auth B] I [auth B] J [auth B] C [auth A], D [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]