4K4R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystallographic Fragment-Based Drug Discovery: Use of a Brominated Fragment Library Targeting HIV Protease.

Tiefenbrunn, T.Forli, S.Happer, M.Gonzalez, A.Tsai, Y.Soltis, M.Elder, J.H.Olson, A.J.Stout, C.D.

(2014) Chem Biol Drug Des 83: 141-148

  • DOI: https://doi.org/10.1111/cbdd.12227
  • Primary Citation of Related Structures:  
    4K4P, 4K4Q, 4K4R

  • PubMed Abstract: 

    A library of 68 brominated fragments was screened against a new crystal form of inhibited HIV-1 protease in order to probe surface sites in soaking experiments. Often, fragments are weak binders with partial occupancy, resulting in weak, difficult-to-fit electron density. The use of a brominated fragment library addresses this challenge, as bromine can be located unequivocally via anomalous scattering. Data collection was carried out in an automated fashion using AutoDrug at SSRL. Novel hits were identified in the known surface sites: 3-bromo-2,6-dimethoxybenzoic acid (Br6) in the flap site and 1-bromo-2-naphthoic acid (Br27) in the exosite, expanding the chemistry of known fragments for development of higher affinity potential allosteric inhibitors. At the same time, mapping the binding sites of a number of weaker binding Br-fragments provides further insight into the nature of these surface pockets.


  • Organizational Affiliation

    Department of Integrative Computational and Structural Biology, TSRI, 10550 N. Torrey Pines Rd., La Jolla, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gag-Pol polyprotein
A, B
99Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)Mutation(s): 1 
Gene Names: gag-pol
EC: 3.4.23.16
UniProt
Find proteins for P12499 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34))
Explore P12499 
Go to UniProtKB:  P12499
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12499
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3TL
Query on 3TL

Download Ideal Coordinates CCD File 
H [auth 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
C50 H64 N6 O10
BJJPNOGMLLUCER-KUTQPOQPSA-N
27B
Query on 27B

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
1-bromonaphthalene-2-carboxylic acid
C11 H7 Br O2
VUVIRKAVBZITDO-UHFFFAOYSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
L [auth B]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
I [auth B],
K [auth B]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3TL BindingDB:  4K4R Ki: 1.5 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.488α = 90
b = 98.488β = 90
c = 96.571γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
autoXDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2014-02-12
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations