1HVK

INFLUENCE OF STEREOCHEMISTRY ON ACTIVITY AND BINDING MODES FOR C2 SYMMETRY-BASED DIOL INHIBITORS OF HIV-1 PROTEASE

• PDB DOI: https://doi.org/10.2210/pdb1HVK/pdb

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


• Deposited: 1994-01-26 Released: 1994-04-30 
• Deposition Author(s): Bhat, T.N., Hosur, M.V., Baldwin, E.T., Erickson, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.177 
• R-Value Observed: 0.177 

Literature

Influence of Stereochemistry on Activity and Binding Modes for C2 Symmetry-Based Diol Inhibitors of HIV-1 Protease

Hosur, M.V., Bhat, T.N., Kempf, D., Baldwin, E.T., Liu, B., Gulnik, S., Wideburg, N.E., Norbeck, D.W., Appelt, K., Erickson, J.W.

(1994) J Am Chem Soc 116: 847-855

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: 22.4 kDa 
• Atom Count: 1,575 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 PROTEASE	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A79	C [auth A]	N-{1-BENZYL-(2S,3S)-2,3-DIHYDROXY-4-[3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRYLAMINO]-5-PHENYL-PENTYL}-3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRAMIDE C44 H58 N8 O6 QPVWMQXBTCSLCB-UNHORJANSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
A79	BindingDB:  1HVK	Ki: min: 0.01, max: 9 (nM) from 3 assay(s)
		Kd: 0.08 (nM) from 1 assay(s)
		IC50: 15 (nM) from 1 assay(s)
	PDBBind:  1HVK	Ki: 0.01 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.177 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.85	α = 90
b = 59.53	β = 90
c = 62.2	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-04-30 
Deposition Author(s): Bhat, T.N., Hosur, M.V., Baldwin, E.T., Erickson, J.W.

Revision History  

• Version 1.0: 1994-04-30
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other