ISDA: 4HDP

Deposition Date 2012-10-02

Release Date 2013-08-14

Last Version Date 2023-09-20

Entry Detail

PDB ID:

4HDP

Keywords:

HYDROLASE/Hydrolase Inhibitor

Title:

Crystal Structure of HIV-1 protease mutants I50V complexed with inhibitor GRL-0519

Biological Source:

Source Organism:

Human immunodeficiency virus type 1 (Taxon ID: 11686)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.22 Å

R-Value Free:

0.20

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 21 21 2

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:HIV-1 Protease
Gene (Uniprot):gag-pol
Mutagens:Q7K, L33I, I50V, L63I, C67A, C95A
Chain IDs:A (auth: B), B (auth: A)
Chain Length:99
Number of Molecules:2
Biological Source:Human immunodeficiency virus type 1

UniProt ID:P03367 Pfam ID:PF00077

Ligand Molecules

G52

Primary Citation

Novel P2 tris-tetrahydrofuran group in antiviral compound 1 (GRL-0519) fills the S2 binding pocket of selected mutants of HIV-1 protease.

Zhang, H, Wang, Y.F, Shen, C.H, Agniswamy, J, Rao, K.V, Xu, C.X, Ghosh, A.K, Harrison, R.W, Weber, I.T.Show

J.Med.Chem. 56 1074 1083 (2013)

PMID: 23298236 DOI: 10.1021/jm301519z

Abstact

GRL-0519 (1) is a potent antiviral inhibitor of HIV-1 protease (PR) possessing tris-tetrahydrofuran (tris-THF) at P2. The high resolution X-ray crystal structures of inhibitor 1 in complexes with single substitution mutants PR(R8Q), PR(D30N), PR(I50V), PR(I54M), and PR(V82A) were analyzed in relation to kinetic data. The smaller valine side chain in PR(I50V) eliminated hydrophobic interactions with inhibitor and the other subunit consistent with 60-fold worse inhibition. Asn30 in PR(D30N) showed altered interactions with neighboring residues and 18-fold worse inhibition. Mutations V82A and I54M showed compensating structural changes consistent with 6-7-fold lower inhibition. Gln8 in PR(R8Q) replaced the ionic interactions of wild type Arg8 with hydrogen bond interactions without changing the inhibition significantly. The carbonyl oxygen of Gly48 showed two alternative conformations in all structures likely due to the snug fit of the large tris-THF group in the S2 subsite in agreement with high antiviral efficacy of 1 on resistant virus.

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