3KFN

HIV Protease (PR) with inhibitor TL-3 and fragment hit 4D9 by soaking

Structural Biology Knowledgebase: 3KFN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.214

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3KFN

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 23155.97

Macromolecule Entities
Molecule Chains Length Organism Details
Protease A, B 99 Human immunodeficiency virus 1 EC#: 5.3.3.14 IUBMB
Mutation: R7K
Gene Name(s): gag-pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
3TL
Query on 3TL

A benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10- dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13- bis(1-methylethyl)-2,5,12,15,18-pentaoxo- 20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos- 1-yl]carbamate
TL-3, C2 symmetric inhibitor (Synonym)
C50 H64 N6 O10
BJJPNOGMLLUCER-KUTQPOQPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
4DX
Query on 4DX

A (1S,2S)-2-methylcyclohexanol
trans-2-methylcyclohexanol (Synonym)
C7 H14 O
NDVWOBYBJYUSMF-BQBZGAKWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A, B DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BME
Query on BME

B BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
3TL N/A in BindingDB
N/A in BindingMoad
IC50: 18000 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000434 (VAL,ALA,PHQ,PHL) A N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.214
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.95 α = 90.00
b = 85.57 β = 90.00
c = 46.49 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-10-27
  • Released Date: 2010-02-23
  • Deposition author(s): Stout, C.D.

Revision History

  • 2013-02-27
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords