1NPA

crystal structure of HIV-1 protease-hup

PDB DOI: https://doi.org/10.2210/pdb1NPA/pdb

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

Deposited: 2003-01-17 Released: 2004-01-27
Deposition Author(s): Smith III, A.B., Hirschmann, R., Pasternak, A., Yao, W., Sprengeler, P.A., Holloway, M.K., Kuo, L.C., Chen, Z., Darke, P.L., Schleif, W.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Work: 0.183
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

An orally bioavailable pyrrolinone inhibitor of HIV-1 protease: computational analysis and X-ray crystal structure of the enzyme complex.

Smith III, A.B., Hirschmann, R., Pasternak, A., Yao, W., Sprengeler, P.A., Holloway, M.K., Kuo, L.C., Chen, Z., Darke, P.L., Schleif, W.A.

(1997) J Med Chem 40: 2440-2444

PubMed: 9258349 Search on PubMed
DOI: https://doi.org/10.1021/jm970195u
Primary Citation of Related Structures:
1NPA

Organizational Affiliation

Department of Chemistry, University of Pennsylvania, Philadelphia 19104, USA.

Macromolecule Content

Total Structure Weight: 22.24 kDa
Atom Count: 1,684
Modelled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POL polyprotein	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: POL EC: 3.4.23.16
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3NH Query on 3NH Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(3S)-TETRAHYDROFURAN-3-YL (1R,2S)-3-[4-((1R)-2-{[(S)-AMINO(HYDROXY)METHYL]OXY}-2,3-DIHYDRO-1H-INDEN-1-YL)-2-BENZYL-3-OXOPYRROLIDIN-2-YL]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE C₃₆ H₄₃ N₃ O₇ BYWKHOXUUACYRY-RJAVELRTSA-N		Interactions Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
3NH	Binding MOAD: 1NPA	IC50: 2 (nM) from 1 assay(s)
3NH	PDBBind: 1NPA	IC50: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Work: 0.183
R-Value Observed: 0.183
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.26	α = 90
b = 87.46	β = 90
c = 46.41	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-01-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-01-27
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations