3HYF

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

PDB DOI: https://doi.org/10.2210/pdb3HYF/pdb

Classification: HYDROLASE
Organism(s): Human immunodeficiency virus 1, Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-22 Released: 2009-10-20
Deposition Author(s): Lansdon, E.B., Kirschberg, T.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.232
R-Value Work: 0.196
R-Value Observed: 0.198

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

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.

(2009) J Med Chem 52: 5781-5784

PubMed: 19791799 Search on PubMed
DOI: https://doi.org/10.1021/jm900597q
Primary Citation of Related Structures:
3HYF

PubMed Abstract:
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.

Organizational Affiliation

Department of Medicinal Chemistry, Gilead Sciences, Foster City, California 94404, USA. tkirschberg@gilead.com

Macromolecule Content

Total Structure Weight: 17.59 kDa
Atom Count: 1,370
Modelled Residue Count: 143
Deposited Residue Count: 150
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/RNaseH	A	150	Human immunodeficiency virus 1, Escherichia coli K-12	Mutation(s): 0 Gene Names: pol, Reverse Transcriptase (amino acids 427-560) EC: 3.1.26.4
UniProt
Find proteins for P0A7Y4 (Escherichia coli (strain K12)) Explore P0A7Y4 Go to UniProtKB: P0A7Y4
Find proteins for Q72547 (Human immunodeficiency virus 1) Explore Q72547 Go to UniProtKB: Q72547
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q72547P0A7Y4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ON1 Query on ON1 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	2-(3,4-dichlorobenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid C₁₂ H₈ Cl₂ N₂ O₄ OZDSTVKQUHMIRA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
ON1	PDBBind: 3HYF	IC50: 1200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.232
R-Value Work: 0.196
R-Value Observed: 0.198
Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.717	α = 90
b = 90.326	β = 90
c = 113.334	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
AMoRE	phasing
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-10-20

Deposition Author(s):

Lansdon, E.B.

Kirschberg, T.A.

Revision History (Full details and data files)

Version 1.0: 2009-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2011-11-16
Changes: Atomic model
Version 1.3: 2017-08-16
Changes: Refinement description, Source and taxonomy
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-03-13
Changes: Source and taxonomy