2CEJ | pdb_00002cej

P1' Extended HIV-1 Protease Inhibitors Encompassing a Tertiary Alcohol in the Transition-State Mimicking Scaffold

PDB DOI: https://doi.org/10.2210/pdb2CEJ/pdb

Classification: HYDROLASE
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-02-07 Released: 2007-02-13
Deposition Author(s): Ginman, N., Ekegren, J.K., Johansson, A., Wallberg, H., Larhed, M., Samuelsson, B., Hallberg, A., Unge, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.277 (Depositor), 0.221 (DCC)
R-Value Work:
0.236 (Depositor), 0.222 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Microwave-Accelerated Synthesis of P1'-Extended HIV-1 Protease Inhibitors Encompassing a Tertiary Alcohol in the Transition-State Mimicking Scaffold

Ekegren, J.K., Ginman, N., Johansson, A., Wallberg, H., Larhed, M., Samuelsson, B., Unge, T., Hallberg, A.

(2006) J Med Chem 49: 1828

PubMed: 16509598 Search on PubMed
DOI: https://doi.org/10.1021/jm051239z
Primary Citation Related Structures:
2CEJ, 2CEM, 2CEN

PubMed Abstract:
Two series of P1'-extended HIV-1 protease inhibitors comprising a tertiary alcohol in the transition-state mimic exhibiting Ki values ranging from 2.1 to 93 nM have been synthesized. Microwave-accelerated palladium-catalyzed cross-couplings were utilized to rapidly optimize the P1' side chain. High cellular antiviral potencies were encountered when the P1' benzyl group was elongated with a 3- or 4-pyridyl substituent (EC50 = 0.18-0.22 microM). X-ray crystallographic data were obtained for three inhibitors cocrystallized with the enzyme.

Organizational Affiliation

Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden.

Macromolecule Content

Total Structure Weight: 22.29 kDa
Atom Count: 1,642
Modeled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POL PROTEIN	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0 EC: 3.4.23.16
UniProt
Find proteins for Q8Q3H0 (Human immunodeficiency virus type 1) Explore Q8Q3H0 Go to UniProtKB: Q8Q3H0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8Q3H0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1AH Query on 1AH Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	3-AMINO-3-BENZYL-[4.3.0]BICYCLO-1,6-DIAZANONAN-2-ONE C₃₄ H₄₁ Br N₄ O₆ JTIFBCHFPVQSEH-UNMGZEBXSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.277 (Depositor), 0.221 (DCC)
R-Value Work: 0.236 (Depositor), 0.222 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.88	α = 90
b = 85.71	β = 90
c = 46.82	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-02-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-02-13
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description