ISDA: 3HYF

Deposition Date 2009-06-22

Release Date 2009-10-20

Last Version Date 2024-03-13

Entry Detail

PDB ID:

3HYF

Keywords:

HYDROLASE

Title:

Crystal structure of HIV-1 RNase H p15 with engineered E. coli loop and active site inhibitor

Biological Source:

Source Organism:

Human immunodeficiency virus 1 (Taxon ID: 11676)
Escherichia coli (Taxon ID: 83333)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.70 Å

R-Value Free:

0.23

R-Value Work:

0.19

R-Value Observed:

0.19

Space Group:

I 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Reverse transcriptase/RNaseH
Gene (Uniprot):rnhA, pol
Chain IDs:A
Chain Length:150
Number of Molecules:1
Biological Source:Human immunodeficiency virus 1, Escherichia coli

UniProt ID:P0A7Y4,Q72547 Pfam ID:PF00075 EC:3.1.13.2

Ligand Molecules

ACT

GOL

ON1

Primary Citation

RNase H active site inhibitors of human immunodeficiency virus type 1 reverse transcriptase: design, biochemical activity, and structural information.

Kirschberg, T.A, Balakrishnan, M, Squires, N.H, Barnes, T, Brendza, K.M, Chen, X, Eisenberg, E.J, Jin, W, Kutty, N, Leavitt, S, Liclican, A, Liu, Q, Liu, X, Mak, J, Perry, J.K, Wang, M, Watkins, W.J, Lansdon, E.B.Show

J.Med.Chem. 52 5781 5784 (2009)

PMID: 19791799 DOI: 10.1021/jm900597q

Abstact

Pyrimidinol carboxylic acids were designed as inhibitors of HIV-1 RNase H function. These molecules can coordinate to two divalent metal ions in the RNase H active site. Inhibition of enzymatic activity was measured in a biochemical assay, but no antiviral effect was observed. Binding was demonstrated via a solid state structure of the isolated p15-Ec domain of HIV-1 RT showing inhibitor and two Mn(II) ions bound to the RNase H active site.

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