4H4M

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with (E)-3-(3-chloro-5-(4-chloro-2-(2-(2,4-dioxo-3,4- dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)phenyl)acrylonitrile (JLJ494), a Non-nucleoside Inhibitor

Structural Biology Knowledgebase: 4H4M SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.233

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4H4M

Classification: Hydrolase / Hydrolase inhibitor

Total Structure Weight: 114536.44

Macromolecule Entities
Molecule Chains Length Organism Details
Reverse transcriptase/ribonuclease H, Exoribonuclease H, p66 RT A 557 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB 2.7.7.7 IUBMB 3.1.13.2 IUBMB 3.1.26.13 IUBMB
Fragment: HIV-1 Reverse Transcriptase, p66 Subunit
Mutation: K172A, K173A, C280S
Gene Name(s): gag-pol
Reverse transcriptase/ribonuclease H, Exoribonuclease H, p51 RT B 428 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB 2.7.7.7 IUBMB 3.1.13.2 IUBMB 3.1.26.13 IUBMB
Fragment: HIV-1 Reverse Transcriptase, p55 Subunit
Mutation: C280S
Gene Name(s): gag-pol

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
494
Query on 494

A (2E)-3-(3-chloro-5-{4-chloro-2-[2-(2,4-dioxo- 3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}phenyl)prop- 2-enenitrile
C21 H15 Cl2 N3 O4
LXPGWIGXHHBGJC-OWOJBTEDSA-N
Ligand Explorer
 
JSmol
EDO
Query on EDO

B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
494 N/A in BindingDB
N/A in BindingMoad
IC50: 3.0 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.233
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 225.13 α = 90.00
b = 69.21 β = 106.43
c = 104.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-17
  • Released Date: 2012-12-05
  • Deposition author(s): Frey, K.M., Anderson, K.S.

Revision History

  • 2013-01-02
    Type: Citation | Details: Citation update