2VG6 | pdb_00002vg6

Crystal structures of HIV-1 reverse transcriptase complexes with thiocarbamate non-nucleoside inhibitors

PDB DOI: https://doi.org/10.2210/pdb2VG6/pdb

Classification: TRANSFERASE
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-08 Released: 2007-12-11
Deposition Author(s): Spallarossa, A., Cesarini, S., Ranise, A., Ponassi, M., Unge, T., Bolognesi, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.01 Å
R-Value Free:
0.335 (Depositor), 0.333 (DCC)
R-Value Work:
0.244 (Depositor), 0.237 (DCC)
R-Value Observed:
0.248 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structures of HIV-1 Reverse Transcriptase Complexes with Thiocarbamate Non-Nucleoside Inhibitors.

Spallarossa, A., Cesarini, S., Ranise, A., Ponassi, M., Unge, T., Bolognesi, M.

(2008) Biochem Biophys Res Commun 365: 764

PubMed: 18035053 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2007.11.036
Primary Citation Related Structures:
2VG5, 2VG6, 2VG7

PubMed Abstract:
O-Phthalimidoethyl-N-arylthiocarbamates (TCs) have been recently identified as a new class of potent HIV-1 reverse transcriptase (RT) non-nucleoside inhibitors (NNRTIs), by means of computer-aided drug design techniques [Ranise A. Spallarossa, S. Cesarini, F. Bondavalli, S. Schenone, O. Bruno, G. Menozzi, P. Fossa, L. Mosti, M. La Colla, et al., Structure-based design, parallel synthesis, structure-activity relationship, and molecular modeling studies of thiocarbamates, new potent non-nucleoside HIV-1 reverse transcriptase inhibitor isosteres of phenethylthiazolylthiourea derivatives, J. Med. Chem. 48 (2005) 3858-3873]. To elucidate the atomic details of RT/TC interaction and validate an earlier TC docking model, the structures of three RT/TC complexes were determined at 2.8-3.0A resolution by X-ray crystallography. The conformations adopted by the enzyme-bound TCs were analyzed and compared with those of bioisosterically related NNRTIs.

Organizational Affiliation

Dipartimento di Scienze Farmaceutiche, Universita' di Genova, viale Benedetto XV, 3, I-16132 Genova, Italy.

Macromolecule Content

Total Structure Weight: 114.62 kDa
Atom Count: 7,856
Modeled Residue Count: 950
Deposited Residue Count: 985
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REVERSE TRANSCRIPTASE/RIBONUCLEASE H	A	557	Human immunodeficiency virus 1	Mutation(s): 0 EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P51 RT	B	428	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NNB Query on NNB 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]	O-[2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl] (4-bromophenyl)thiocarbamate C₁₇ H₁₃ Br N₂ O₃ S BDVAWAILQCYMQE-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.01 Å
R-Value Free: 0.335 (Depositor), 0.333 (DCC)
R-Value Work: 0.244 (Depositor), 0.237 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.591	α = 90
b = 157.183	β = 90
c = 154.921	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-12-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-12-11
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-01-17
Changes: Data collection
Version 1.4: 2024-05-08
Changes: Data collection, Database references, Other