7L2Y | pdb_00007l2y

HIV Integrase core domain in complex with inhibitor 2-(5-(3-fluorophenyl)-2-(2-(thiophen-2-yl)ethynyl)-1- benzofuran-3-yl)ethanoic acid

PDB DOI: https://doi.org/10.2210/pdb7L2Y/pdb

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

Deposited: 2020-12-17 Released: 2021-12-22
Deposition Author(s): Gorman, M.A., Parker, M.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.249 (Depositor), 0.255 (DCC)
R-Value Work:
0.209 (Depositor), 0.217 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 7L2Y

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

HIV Integrase core domain in complex with inhibitor

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

To be published.

Macromolecule Content

Total Structure Weight: 19.16 kDa
Atom Count: 1,170
Modeled Residue Count: 139
Deposited Residue Count: 162
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A [auth AAA]	162	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: pol
UniProt
Find proteins for F2WR52 (Human immunodeficiency virus type 1) Explore F2WR52 Go to UniProtKB: F2WR52
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2WR52
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XHY (Subject of Investigation/LOI) Query on XHY Download:Ideal Coordinates CCD File SDF format, chain J [auth AAA] MOL2 format, chain J [auth AAA] mmCIF format, chain J [auth AAA]	J [auth AAA]	4-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzoic acid C₂₀ H₁₄ O₅ ZUPRDSGKERROAH-UHFFFAOYSA-N		Interactions Focus chain J [auth AAA] Interactions & Density Focus chain J [auth AAA]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain I [auth AAA] SDF format, chain H [auth AAA] SDF format, chain G [auth AAA] SDF format, chain F [auth AAA] SDF format, chain E [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth AAA] SDF format, chain D [auth AAA] SDF format, chain C [auth AAA] SDF format, chain B [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain C [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain C [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA], C [auth AAA], D [auth AAA], K [auth AAA]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain K [auth AAA] Interactions & Density Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain K [auth AAA]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS Query on OCS	A [auth AAA]	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.249 (Depositor), 0.255 (DCC)
R-Value Work: 0.209 (Depositor), 0.217 (DCC)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.98	α = 90
b = 45.98	β = 90
c = 138.87	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-12-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-12-22
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.