HIV-1 proteinase complexed with RO 31-8959

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere.

Krohn, A.Redshaw, S.Ritchie, J.C.Graves, B.J.Hatada, M.H.

(1991) J Med Chem 34: 3340-3342

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 PROTEASEA, B99Human immunodeficiency virus type 1 (CLONE 12)Mutation(s): 0 
Gene Names: POL
EC: (PDB Primary Data), (UniProt), (UniProt), (UniProt), (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on ROC

Download Ideal Coordinates CCD File 
C [auth A](2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide
C38 H50 N6 O5
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ROC BindingDB:  1HXB Ki: min: 0.04, max: 138 (nM) from 29 assay(s)
Kd: min: 0.31, max: 67 (nM) from 6 assay(s)
IC50: min: 0.05, max: 270 (nM) from 18 assay(s)
-TΔS: min: -8.03e+1, max: -2.80e+1 (kJ/mol) from 46 assay(s)
ΔH: min: -3.18e+1, max: 43.47 (kJ/mol) from 47 assay(s)
ΔG: min: -6.23e+1, max: -3.55e+1 (kJ/mol) from 44 assay(s)
Binding MOAD:  1HXB Ki: 0.12 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000454 (ROC)
Query on PRD_000454
C [auth A]SaquinavirPeptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.31α = 90
b = 63.31β = 90
c = 83.45γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-03-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other