4H4O | pdb_00004h4o

Crystal Structure of HIV-1 Reverse Transcriptase (RT) in Complex with (E)-3-(3-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)- 4-fluorophenoxy)-5-fluorophenyl)acrylonitrile (JLJ506), A Non-nucleoside inhibitor

PDB DOI: https://doi.org/10.2210/pdb4H4O/pdb

Classification: Hydrolase/Hydrolase inhibitor
Organism(s): Human immunodeficiency virus type 1 BH10
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-09-17 Released: 2012-12-05
Deposition Author(s): Frey, K.M., Anderson, K.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.265 (Depositor), 0.263 (DCC)
R-Value Work:
0.232 (Depositor), 0.233 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structures of HIV-1 Reverse Transcriptase with Picomolar Inhibitors Reveal Key Interactions for Drug Design.

Frey, K.M., Bollini, M., Mislak, A.C., Cisneros, J.A., Gallardo-Macias, R., Jorgensen, W.L., Anderson, K.S.

(2012) J Am Chem Soc 134: 19501-19503

PubMed: 23163887 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ja3092642
Primary Citation Related Structures:
4H4M, 4H4O

PubMed Abstract:
X-ray crystal structures at 2.9 Å resolution are reported for two complexes of catechol diethers with HIV-1 reverse transcriptase. The results help elucidate the structural origins of the extreme antiviral activity of the compounds. The possibility of halogen bonding between the inhibitors and Pro95 is addressed. Structural analysis reveals key interactions with conserved residues P95 and W229 of importance for design of inhibitors with high potency and favorable resistance profiles.

Organizational Affiliation

Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States.

Macromolecule Content

Total Structure Weight: 114.44 kDa
Atom Count: 8,082
Modeled Residue Count: 977
Deposited Residue Count: 985
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H, Exoribonuclease H, p66 RT	A	557	Human immunodeficiency virus type 1 BH10	Mutation(s): 3 Gene Names: p66 RT EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H, Exoribonuclease H, p51 RT	B	428	Human immunodeficiency virus type 1 BH10	Mutation(s): 1 Gene Names: p51 RT EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
506 Query on 506 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]	(2E)-3-(3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]-4-fluorophenoxy}-5-fluorophenyl)prop-2-enenitrile C₂₁ H₁₅ F₂ N₃ O₄ USRHSVZSPKDGMT-OWOJBTEDSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
506	BindingDB: 4H4O	IC50: 2.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.265 (Depositor), 0.263 (DCC)
R-Value Work: 0.232 (Depositor), 0.233 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.451	α = 90
b = 69.575	β = 106.21
c = 104.401	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-12-05

Deposition Author(s):

Frey, K.M.

Anderson, K.S.

Revision History (Full details and data files)

Version 1.0: 2012-12-05
Type: Initial release
Version 1.1: 2013-01-02
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description