4ZIP: HIV-1 wild Type protease with GRL-0648A

HIV-1 wild Type protease with GRL-0648A (a isophthalamide-derived P2-Ligand). Determined by X-ray diffraction at 1.11 Å resolution. Released 15 Jul 2015.

Method: X-ray diffraction
Resolution: 1.11 Å
Organism: Human immunodeficiency virus type 1
Chains: 2
Atoms: 2,037
Mol. weight: 22.44 kDa
Ligands: G64
Released: 15 Jul 2015

Explore 4ZIP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ZIP contains 3 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: 2 helices, 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	42-49	8	2
β-strand	52-66	15	2
β-strand	69-77	9	2
β-strand	84-85	2	2
α-helix	87-90	4
α-helix	91-93	3
β-strand	96-98	3	1

Chain B: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	10-15	6	3
β-strand	18-24	7	3
β-strand	32-33	2	3
β-strand	43-49	7	3
β-strand	52-66	15	3
β-strand	69-77	9	3
β-strand	84-85	2	3
α-helix	87-90	4
β-strand	96-98	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease	A, B	protein	99	Human immunodeficiency virus type 1	P03366

Sequence of entity 1 (A, B), FASTA

>4ZIP_1 Protease (chains A, B)
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYD
QIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligands and cofactors

ID	Name	Formula	Copies
G64	N-[(2,5-dimethyl-1,3-oxazol-4-yl)methyl]-N'-[(2S,3R)-3-hydroxy-4-{[(4-methoxyph…	C37 H46 N4 O7 S	1

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

Primary citation

Structure-based design, synthesis, X-ray studies, and biological evaluation of novel HIV-1 protease inhibitors containing isophthalamide-derived P2-ligands. Ghosh, A.K., Takayama, J., Kassekert, L.A. et al. Bioorg Med Chem Lett (2015) 25:4903-4909. DOI 10.1016/j.bmcl.2015.05.052 · 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…
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
5AGZ 1.2 Å, Disubstituted bis-THF moieties as new P2 ligands in non-peptidal HIV- 1 Protease…
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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