8ESX | pdb_00008esx

HIV protease in complex with benzoxaborolone analog of darunavir

PDB DOI: https://doi.org/10.2210/pdb8ESX/pdb

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

Deposited: 2022-10-15 Released: 2023-02-08
Deposition Author(s): Windsor, I.W., Graham, B.J., Raines, R.T.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.206 (Depositor), 0.206 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Inhibition of HIV-1 Protease by a Boronic Acid with High Oxidative Stability.

Graham, B.J., Windsor, I.W., Raines, R.T.

(2023) ACS Med Chem Lett 14: 171-175

PubMed: 36793428 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.2c00464
Primary Citation Related Structures:
8ESX, 8ESY

PubMed Abstract:
HIV-1 protease is an important target for pharmaceutical intervention in HIV infection. Extensive structure-based drug design led to darunavir becoming a key chemotherapeutic agent. We replaced the aniline group of darunavir with a benzoxaborolone to form BOL-darunavir. This analogue has the same potency as darunavir as an inhibitor of catalysis by wild-type HIV-1 protease and, unlike darunavir, does not lose potency as an inhibitor of the common D30N variant. Moreover, BOL-darunavir is much more stable to oxidation than is a simple phenylboronic acid analogue of darunavir. X-ray crystallography revealed an extensive network of hydrogen bonds between the enzyme and benzoxaborolone moiety, including a novel direct hydrogen bond from a main-chain nitrogen to the carbonyl oxygen of the benzoxaborolone moiety that displaces a water molecule. These data highlight the utility of benzoxaborolone as a pharmacophore.

Organizational Affiliation

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.

Macromolecule Content

Total Structure Weight: 22.38 kDa
Atom Count: 1,836
Modeled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 5 Gene Names: pol
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585 Go to UniProtKB: P04585
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04585
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
X7B (Subject of Investigation/LOI) Query on X7B Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	[(3~{a}~{S},4~{R},6~{a}~{R})-2,3,3~{a},4,5,6~{a}-hexahydrofuro[2,3-b]furan-4-yl] ~{N}-[(2~{S},3~{R})-4-[[7,7-bis(oxidanyl)-9-oxidanylidene-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-3-yl]sulfonyl-(2-methylpropyl)amino]-3-oxidanyl-1-phenyl-butan-2-yl]carbamate C₂₈ H₃₆ B N₂ O₁₁ S YAKWEBDNMFOPCT-AYENOPNPSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]