4RVI

Crystal structure of multidrug-resistant clinical isolate A02 HIV-1 protease in complex with non-peptidic inhibitor, GRL0519

PDB DOI: https://doi.org/10.2210/pdb4RVI/pdb

Classification: hydrolase/hydrolase inhibitor
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-11-26 Released: 2016-05-04
Deposition Author(s): Yedidi, R.S., Garimella, H., Kaufman, J.D., Das, D., Wingfield, P.T., Ghosh, A.K., Mitsuya, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.277
R-Value Work: 0.231
R-Value Observed: 0.234

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Enhanced antiviral activity by the P2-tris-tetrahydrofuran moiety of GRL-0519, a novel nonpeptidic HIV-1 protease inhibitor (PI), against multi-PI-resistant and highly darunavir-resistant strains of HIV-1

Yedidi, R.S., Maeda, K., Aoki, M., Garimella, H., Rao, K.V., Akasapu, S., Davis, D.A., Kaufman, J.D., Das, D., Wingfield, P.T., Amano, M., Ghosh, A.K., Mitsuya, H.

To be published.

Macromolecule Content

Total Structure Weight: 44.57 kDa
Atom Count: 3,413
Modelled Residue Count: 396
Deposited Residue Count: 396
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 protease	A, B, C, D	99	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: pol
UniProt
Find proteins for Q9J006 (Human immunodeficiency virus 1) Explore Q9J006 Go to UniProtKB: Q9J006
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9J006
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G52 Query on G52 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth C]	E [auth A], F [auth C]	(3R,3aS,3bR,6aS,7aS)-octahydrodifuro[2,3-b:3',2'-d]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}propyl]carbamate C₃₀ H₄₀ N₂ O₉ S QWMNYFXRFHGYGS-DDGGWZRMSA-N		Interactions Focus chain E [auth A] Focus chain F [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.277
R-Value Work: 0.231
R-Value Observed: 0.234
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.96	α = 90
b = 64.73	β = 90
c = 100.74	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-05-04

Deposition Author(s):

Wingfield, P.T.

Revision History (Full details and data files)

Version 1.0: 2016-05-04
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.