1D4Y | pdb_00001d4y

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.216 (Depositor)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1D4Y

This is version 1.6 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1021/jm960541s
Primary Citation Related Structures:
1D4S, 1D4Y

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03367
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPV Query on TPV Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.216 (Depositor)
R-Value Observed: 0.174 (Depositor)

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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 1999-10-13

Deposition Author(s):

Watenpaugh, K.D.

Janakiraman, M.N.

Revision History (Full details and data files)

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