3ST5 | pdb_00003st5

Crystal structure of wild-type HIV-1 protease with C3-Substituted Hexahydrocyclopentafuranyl Urethane as P2-Ligand, GRL-0489A

PDB DOI: https://doi.org/10.2210/pdb3ST5/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Human immunodeficiency virus type 1 (BRU ISOLATE)
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-07-08 Released: 2011-08-17
Deposition Author(s): Wang, Y.-F., Agniswamy, J., Weber, I.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.219 (Depositor), 0.211 (DCC)
R-Value Work:
0.157 (Depositor), 0.163 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Design of HIV-1 Protease Inhibitors with C3-Substituted Hexahydrocyclopentafuranyl Urethanes as P2-Ligands: Synthesis, Biological Evaluation, and Protein-Ligand X-ray Crystal Structure.

Ghosh, A.K., Chapsal, B.D., Parham, G.L., Steffey, M., Agniswamy, J., Wang, Y.F., Amano, M., Weber, I.T., Mitsuya, H.

(2011) J Med Chem 54: 5890-5901

PubMed: 21800876 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jm200649p
Primary Citation Related Structures:
3ST5

PubMed Abstract:
We report the design, synthesis, biological evaluation, and the X-ray crystal structure of a novel inhibitor bound to the HIV-1 protease. Various C3-functionalized cyclopentanyltetrahydrofurans (Cp-THF) were designed to interact with the flap Gly48 carbonyl or amide NH in the S2-subsite of the HIV-1 protease. We investigated the potential of those functionalized ligands in combination with hydroxyethylsulfonamide isosteres. Inhibitor 26 containing a 3-(R)-hydroxyl group on the Cp-THF core displayed the most potent enzyme inhibitory and antiviral activity. Our studies revealed a preference for the 3-(R)-configuration over the corresponding 3-(S)-derivative. Inhibitor 26 exhibited potent activity against a panel of multidrug-resistant HIV-1 variants. A high resolution X-ray structure of 26-bound HIV-1 protease revealed important molecular insight into the ligand-binding site interactions.

Organizational Affiliation

Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA. akghosh@purdue.edu

Macromolecule Content

Total Structure Weight: 22.13 kDa
Atom Count: 1,874
Modeled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus type 1 (BRU ISOLATE)	Mutation(s): 5 Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367 Go to UniProtKB: P03367
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03367
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G89 Query on G89 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	(3R,3aR,5R,6aR)-3-hydroxyhexahydro-2H-cyclopenta[b]furan-5-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate C₂₉ H₄₀ N₂ O₈ S LJPOEDMTSRUIGG-RVSUYJHDSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000798 (G89) Query on PRD_000798	D [auth B]	(3R,3AR,5R,6AR)-3-HYDROXYHEXAHYDRO-2H-CYCLOPENTA[B]FURAN-5-YL [(2S,3R)-3-HYDROXY-4-{[(4-METHOXYPHENYL)SULFONYL](2-METHYLPROPYL)AMINO}-1-PHENYLBUTAN-2-YL]CARBAMATE	Peptide-like / Enzyme inhibitor		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.219 (Depositor), 0.211 (DCC)
R-Value Work: 0.157 (Depositor), 0.163 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.39	α = 90
b = 86.552	β = 90
c = 45.846	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-08-17

Deposition Author(s):

Wang, Y.-F.

Agniswamy, J.

Weber, I.T.

Revision History (Full details and data files)

Version 1.0: 2011-08-17
Type: Initial release
Version 1.1: 2011-08-31
Changes: Database references
Version 1.2: 2012-12-12
Changes: Other
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description