4K4R

TL-3 inhibited Trp6Ala HIV Protease with 1-bromo-2-napthoic acid bound in exosite

Structural Biology Knowledgebase: 4K4R SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4K4R

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 23312.91

Macromolecule Entities
Molecule Chains Length Organism Details
Gag-Pol polyprotein A, B 99 Human immunodeficiency virus 1 EC#: 5.3.3.14 IUBMB
Mutation: W6A, Q7K, K41R
Gene Name(s): gag-pol

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)
27B
Query on 27B

A, B 1-bromonaphthalene-2-carboxylic acid
C11 H7 Br O2
VUVIRKAVBZITDO-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BR
Query on BR

B BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NO3
Query on NO3

A, B NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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: 1.8 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.195
  • Space Group: I 41 2 2

Unit Cell:

Length (Å) Angle (°)
a = 98.49 α = 90.00
b = 98.49 β = 90.00
c = 96.57 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-12
  • Released Date: 2013-09-18
  • Deposition author(s): Tiefenbrunn, T., Stout, C.D.

Revision History

  • 2014-02-12
    Type: Citation | Details: Citation update