4I7F | pdb_00004i7f

HIV-1 Reverse Transcriptase in complex with a phosphonate analog of nevirapine

PDB DOI: https://doi.org/10.2210/pdb4I7F/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): HIV-1 M:B_HXB2R
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-11-30 Released: 2013-02-20
Deposition Author(s): Lansdon, E.B., Parrish, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.267 (Depositor), 0.262 (DCC)
R-Value Work:
0.221 (Depositor), 0.215 (DCC)

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

Synthesis and biological evaluation of phosphonate analogues of nevirapine.

Parrish, J., Tong, L., Wang, M., Chen, X., Lansdon, E.B., Cannizzaro, C., Zheng, X., Desai, M.C., Xu, L.

(2013) Bioorg Med Chem Lett 23: 1493-1497

PubMed: 23375792 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2012.12.049
Primary Citation Related Structures:
4I7F

PubMed Abstract:
A series of nevirapine-based analogues containing the phosphonate functionality were prepared and evaluated in vitro against HIV RT. The effect of the phosphonate was evaluated against the wild type and Y181C HIV replication. An in vivo PK study was performed on a select analogue.

Organizational Affiliation

Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA. Jay.Parrish@gilead.com

Macromolecule Content

Total Structure Weight: 116.97 kDa
Atom Count: 7,999
Modeled Residue Count: 957
Deposited Residue Count: 1,000
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase	A	560	HIV-1 M:B_HXB2R	Mutation(s): 0 Gene Names: gag-pol, reverse transcriptase EC: 2.7.7.49
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585 Go to UniProtKB: P04585
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04585
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase	B	440	HIV-1 M:B_HXB2R	Mutation(s): 0 Gene Names: gag-pol, reverse transcriptase EC: 2.7.7.49
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585 Go to UniProtKB: P04585
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04585
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NVE Query on NVE 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]	diethyl ({4-[2-(11-ethyl-5-methyl-6-oxo-6,11-dihydro-5H-dipyrido[3,2-b:2',3'-e][1,4]diazepin-8-yl)ethyl]phenoxy}methyl)phosphonate C₂₇ H₃₃ N₄ O₅ P YVBXNGRTCURFDW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B]	I [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.267 (Depositor), 0.262 (DCC)
R-Value Work: 0.221 (Depositor), 0.215 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.319	α = 90
b = 154.703	β = 90
c = 154.25	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-02-20

Deposition Author(s):

Lansdon, E.B.

Parrish, J.

Revision History (Full details and data files)

Version 1.0: 2013-02-20
Type: Initial release
Version 1.1: 2013-03-06
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