4KO0 | pdb_00004ko0

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX WITH an anilinylpyrimidine derivative (JLJ-135)

PDB DOI: https://doi.org/10.2210/pdb4KO0/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Human immunodeficiency virus type 1 BH10
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-05-10 Released: 2013-08-14
Deposition Author(s): Das, K., Bauman, J.D., Arnold, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.275 (Depositor), 0.270 (DCC)
R-Value Work:
0.237 (Depositor), 0.230 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Extension into the entrance channel of HIV-1 reverse transcriptase-Crystallography and enhanced solubility.

Bollini, M., Frey, K.M., Cisneros, J.A., Spasov, K.A., Das, K., Bauman, J.D., Arnold, E., Anderson, K.S., Jorgensen, W.L.

(2013) Bioorg Med Chem Lett 23: 5209-5212

PubMed: 23899617 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.bmcl.2013.06.093
Primary Citation of Related Structures:
4KKO, 4KO0

PubMed Abstract:
Non-nucleoside inhibitors of HIV-1 reverse transcriptase (HIV-RT) are reported that feature extension into the entrance channel near Glu138. Complexes of the parent anilinylpyrimidine 1 and the morpholinoethoxy analog 2j with HIV-RT have received crystallographic characterization confirming the designs. Measurement of aqueous solubilities of 2j, 2k, the parent triazene 2a, and other NNRTIs demonstrate profound benefits for addition of the morpholinyl substituent.

Organizational Affiliation

Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.

Macromolecule Content

Total Structure Weight: 114.66 kDa
Atom Count: 8,309
Modeled Residue Count: 966
Deposited Residue Count: 985
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 reverse transcriptase, p66 subunit	A	557	Human immunodeficiency virus type 1 BH10	Mutation(s): 3 Gene Names: gag-pol EC: 2.7.7.49
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 reverse transcriptase, p51 subunit	B	428	Human immunodeficiency virus type 1 BH10	Mutation(s): 1 Gene Names: gag-pol EC: 2.7.7.49
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JLJ Query on JLJ 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]	4-[(4-methoxypyrimidin-2-yl)amino]-2-[(3-methylbut-2-en-1-yl)oxy]benzonitrile C₁₇ H₁₈ N₄ O₂ VFPQRVJYEMSZLR-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] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B]	F [auth A], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.275 (Depositor), 0.270 (DCC)
R-Value Work: 0.237 (Depositor), 0.230 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.209	α = 90
b = 73.95	β = 100.23
c = 109.202	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	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: 2013-08-14

Deposition Author(s):

Das, K.

Bauman, J.D.

Arnold, E.

Revision History (Full details and data files)

Version 1.0: 2013-08-14
Type: Initial release
Version 1.1: 2013-09-04
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description