1D4Y

HIV-1 PROTEASE TRIPLE MUTANT/TIPRANAVIR COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1D4Y/pdb

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


• Deposited: 1999-10-06 Released: 1999-10-13 
• Deposition Author(s): Watenpaugh, K.D., Janakiraman, M.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.216 
• R-Value Observed: 0.174 

Literature

Structure-based design of HIV protease inhibitors: sulfonamide-containing 5,6-dihydro-4-hydroxy-2-pyrones as non-peptidic inhibitors.

Thaisrivongs, S., Skulnick, H.I., Turner, S.R., Strohbach, J.W., Tommasi, R.A., Johnson, P.D., Aristoff, P.A., Judge, T.M., Gammill, R.B., Morris, J.K., Romines, K.R., Chrusciel, R.A., Hinshaw, R.R., Chong, K.T., Tarpley, W.G., Poppe, S.M., Slade, D.E., Lynn, J.C., Horng, M.M., Tomich, P.K., Seest, E.P., Dolak, L.A., Howe, W.J., Howard, G.M., Watenpaugh, K.D.

(1996) J Med Chem 39: 4349-4353

• PubMed: 8893827 
• DOI: https://doi.org/10.1021/jm960541s
• Primary Citation of Related Structures:  
  1D4S, 1D4Y

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Organizational Affiliation: 

Upjohn, Inc., Kalamazoo, Michigan 49001, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 22.21 kDa 
• Atom Count: 1,737 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HIV-1 PROTEASE)	A, B	99	Human immunodeficiency virus 1	Mutation(s): 3  EC: 3.4.23.16
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367  Go to UniProtKB:  P03367

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPV	C [auth A]	N-(3-{(1R)-1-[(6R)-4-HYDROXY-2-OXO-6-PHENETHYL-6-PROPYL-5,6-DIHYDRO-2H-PYRAN-3-YL]PROPYL}PHENYL)-5-(TRIFLUOROMETHYL)-2-PYRIDINESULFONAMIDE C31 H33 F3 N2 O5 S SUJUHGSWHZTSEU-FYBSXPHGSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TPV	PDBBind:  1D4Y	Ki: 8.00e-3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.216 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.785	α = 90
b = 87.503	β = 90
c = 46.458	γ = 90

Software Package:

Software Name	Purpose
MERLOT	phasing
SHELXL-97	refinement
X-GEN	data reduction
X-GEN	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-10-13 
Deposition Author(s): Watenpaugh, K.D., Janakiraman, M.N.

Revision History  

• Version 1.0: 1999-10-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-02-22
  Changes: Database references
• Version 1.4: 2017-10-04
  Changes: Refinement description
• Version 1.5: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.6: 2024-02-07
  Changes: Data collection