Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 22.64 kDa 
• Atom Count: 1694 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

2Q5K

Crystal structure of lopinavir bound to wild type HIV-1 protease

• DOI: 10.2210/pdb2Q5K/pdb

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


• Deposited: 2007-06-01 Released: 2007-09-04 
• Deposition Author(s): Schiffer, C.A., Nalam, M.N.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.236 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Design and Synthesis of HIV-1 Protease Inhibitors Incorporating Oxazolidinones as P2/P2' Ligands in Pseudosymmetric Dipeptide Isosteres.

Reddy, G.S., Ali, A., Nalam, M.N., Anjum, S.G., Cao, H., Nathans, R.S., Schiffer, C.A., Rana, T.M.

(2007) J Med Chem 50: 4316-4328

• PubMed: 17696512 
• DOI: 10.1021/jm070284z
• Primary Citation of Related Structures:  
  2Q54, 2Q55, 2Q5K


• PubMed Abstract: 
  

A series of novel HIV-1 protease inhibitors based on two pseudosymmetric dipeptide isosteres have been synthesized and evaluated. The inhibitors were designed by incorporating N-phenyloxazolidinone-5-carboxamides into the hydroxyethylene and (hydroxyethyl)hydrazine dipeptide isosteres as P2 and P2' ligands. Compounds with (S)-phenyloxazolidinones attached at a position proximal to the central hydroxyl group showed low nM inhibitory activities against wild-type HIV-1 protease. Selected compounds were further evaluated for their inhibitory activities against a panel of multidrug-resistant protease variants and for their antiviral potencies in MT-4 cells. The crystal structures of lopinavir (LPV) and two new inhibitors containing phenyloxazolidinone-based ligands in complex with wild-type HIV-1 protease have been determined. A comparison of the inhibitor-protease structures with the LPV-protease structure provides valuable insight into the binding mode of the new inhibitors to the protease enzyme. Based on the crystal structures and knowledge of structure-activity relationships, new inhibitors can be designed with enhanced enzyme inhibitory and antiviral potencies.

---

Organizational Affiliation: 

Chemical Biology Program and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: pol
UniProt
Find proteins for O38710 (Human immunodeficiency virus 1) Explore O38710  Go to UniProtKB:  O38710

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AB1 (Subject of Investigation/LOI)	F [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
PO4	C [auth A], D [auth A], E [auth A], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
AB1	BindingDB:  2Q5K	Ki: min: 5.00e-3, max: 16 (nM) from 7 assay(s)
		Kd: 1.30e-3 (nM) from 1 assay(s)
		IC50: min: 2.5, max: 25 (nM) from 2 assay(s)
		EC50: 1160 (nM) from 1 assay(s)
	Binding MOAD:  2Q5K	Ki: 5.00e-3 (nM) from 1 assay(s)
	PDBBind:  2Q5K	Ki: 5.00e-3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.236 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.343	α = 90
b = 58.043	β = 90
c = 61.133	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2007-06-01 
• Released Date: 2007-09-04 
Deposition Author(s): Schiffer, C.A., Nalam, M.N.L.

Revision History  

• Version 1.0: 2007-09-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Derived calculations, Refinement description, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations, Structure summary