5AGZ: Protease

Disubstituted bis-THF moieties as new P2 ligands in non-peptidal HIV- 1 Protease Inhibitors (II). Determined by X-ray diffraction at 1.2 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 1.2 Å
Organism: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (Z2/CDC-Z34 ISOLATE)
Chains: 2
Atoms: 1,906
Mol. weight: 22.33 kDa
Ligands: QHA
Released: 6 May 2015

Explore 5AGZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5AGZ contains 2 α-helices and 18 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	10-15	6	2
β-strand	18-24	7	2
β-strand	31-33	3	2
β-strand	42-47	6	2
β-strand	54-66	13	2
β-strand	69-77	9	2
β-strand	84-85	2	2
α-helix	87-90	4
β-strand	96-98	3	1

Chain B: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	102-103	2	1
β-strand	110-115	6	3
β-strand	118-124	7	3
β-strand	132-133	2	3
β-strand	143-149	7	3
β-strand	152-166	15	3
β-strand	169-177	9	3
β-strand	184-185	2	3
α-helix	187-190	4
β-strand	196-198	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease	A, B	protein	99	HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (Z2/CDC-Z34 ISOLATE)	P03366

Sequence of entity 1 (A, B), FASTA

>5AGZ_1 PROTEASE (chains A, B)
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD
QIPIEICGHKAIGTVLVGPTPTNVIGRNLLTQIGCTLNF

Ligands and cofactors

ID	Name	Formula	Copies
QHA	(3R,3aS,4R,6aR)-4-[(2-fluoroprop-2-en-1-yl)oxy]hexahydrofuro[2,3-b]furan-3-yl…	C32 H41 F N4 O9 S	1

Water and common crystallization additives (CL) are not listed.

Primary citation

Disubstituted Bis-Thf Moieties as New P2 Ligands in Non-Peptidal HIV-1 Protease Inhibitors (II). Hohlfeld, K., Wegner, J., Kesteleyn, B. et al. J Med Chem (2015) 58:4029. DOI 10.1021/ACS.JMEDCHEM.5B00358 · PubMed

Other PDB entries of the same protein (UniProt P03366), best resolution first:

2HS1 0.84 Å, Ultra-high resolution X-ray crystal structure of HIV-1 protease V32I mutant with TMC114…
3NU3 1.02 Å, Wild Type HIV-1 Protease with Antiviral Drug Amprenavir
2IDW 1.1 Å, Crystal structure analysis of HIV-1 protease mutant V82A with a potent non-peptide…
4ZIP 1.11 Å, HIV-1 wild Type protease with GRL-0648A (a isophthalamide-derived P2-Ligand)
3NU6 1.16 Å, Crystal Structure of HIV-1 Protease Mutant I54M with Antiviral Drug Amprenavir
5JG1 1.16 Å, HIV-1 wild Type protease with GRL-031-14A (a Adamantane P1-Ligand with…
3NU4 1.2 Å, Crystal Structure of HIV-1 Protease Mutant V32I with Antiviral Drug Amprenavir
6PRF 1.21 Å, HIV-1 Protease multiple drug resistant clinical isolate mutant PR20 with GRL-14213A
2HS2 1.22 Å, Crystal structure of M46L mutant of HIV-1 protease complexed with TMC114 (darunavir)
5AH8 1.26 Å, Disubstituted bis-THF moieties as new P2 ligands in non-peptidal HIV- 1 Protease…
3OK9 1.27 Å, Crystal structure of wild-type HIV-1 protease with new oxatricyclic designed inhibitor…
5UPZ 1.27 Å, HIV-1 wild Type protease with GRL-0518A , an isophthalamide-derived P2-P3 ligand with…

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