4L1A | pdb_00004l1a

Crystallographic study of multi-drug resistant HIV-1 protease Lopinavir complex: mechanism of drug recognition and resistance

PDB DOI: https://doi.org/10.2210/pdb4L1A/pdb

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

Deposited: 2013-06-03 Released: 2014-04-02
Deposition Author(s): Liu, Z., Yedidi, R.S., Wang, Y., Dewdney, T., Reiter, S., Brunzelle, J., Kovari, I., Kovari, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.260 (Depositor), 0.258 (DCC)
R-Value Work:
0.197 (Depositor), 0.195 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystallographic study of multi-drug resistant HIV-1 protease lopinavir complex: mechanism of drug recognition and resistance.

Liu, Z., Yedidi, R.S., Wang, Y., Dewdney, T.G., Reiter, S.J., Brunzelle, J.S., Kovari, I.A., Kovari, L.C.

(2013) Biochem Biophys Res Commun 437: 199-204

PubMed: 23792096 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.bbrc.2013.06.027
Primary Citation Related Structures:
4L1A

PubMed Abstract:
Lopinavir (LPV) is a second generation HIV-1 protease inhibitor. Drug resistance has rapidly emerged against LPV since its US FDA approval on September 15, 2000. Mutations at residues 32I, L33F, 46I, 47A, I54V, V82A, I84V, and L90M render the protease drug resistant against LPV. We report the crystal structure of a clinical isolate multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, and 90) complexed with LPV and the in vitro enzymatic IC50 of LPV against MDR 769. The structural and functional studies demonstrate significant drug resistance of MDR 769 against LPV, arising from reduced interactions between LPV and the protease target.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, United States.

Macromolecule Content

Total Structure Weight: 22.17 kDa
Atom Count: 1,782
Modeled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MDR769 HIV-1 protease	A	99	Human immunodeficiency virus 1	Mutation(s): 4 Gene Names: pol
UniProt
Find proteins for Q000H7 (Human immunodeficiency virus type 1) Explore Q000H7 Go to UniProtKB: Q000H7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q000H7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MDR769 HIV-1 protease	B	99	Human immunodeficiency virus 1	Mutation(s): 5 Gene Names: pol
UniProt
Find proteins for Q000H7 (Human immunodeficiency virus type 1) Explore Q000H7 Go to UniProtKB: Q000H7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q000H7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AB1 Query on AB1 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]	N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE C₃₇ H₄₈ N₄ O₅ KJHKTHWMRKYKJE-SUGCFTRWSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.260 (Depositor), 0.258 (DCC)
R-Value Work: 0.197 (Depositor), 0.195 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.828	α = 90
b = 43.828	β = 90
c = 101.805	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-04-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-02
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Structure summary