2ZD1

Crystal Structure of HIV-1 Reverse Transcriptase (RT) in Complex with TMC278 (Rilpivirine), A Non-nucleoside RT Inhibitor

Structural Biology Knowledgebase: 2ZD1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.220

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ZD1

Classification: TRANSFERASE HYDROLASE / INHIBITOR

Total Structure Weight: 114554.65

Macromolecule Entities
Molecule Chains Length Organism Details
Reverse transcriptase/ribonuclease H A 557 Human immunodeficiency virus 1 EC#: 2.7.7.49 IUBMB 2.7.7.7 IUBMB 3.1.26.4 IUBMB
Fragment: P66
Mutation: K172A, K173A, C280S
Gene Name(s): gag-pol
p51 RT B 428 Human immunodeficiency virus 1 Fragment: P51
Mutation: C280S
Gene Name(s): gag-pol

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
T27
Query on T27

A 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin- 2-yl]amino}benzonitrile
Rilpivirine (Synonym)
C22 H18 N6
YIBOMRUWOWDFLG-ONEGZZNKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.220
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 163.37 α = 90.00
b = 73.26 β = 100.07
c = 110.07 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-11-16
  • Released Date: 2008-02-12
  • Deposition author(s): Das, K., Bauman, J.D., Clark Jr., A.D., Shatkin, A.J., Arnold, E.

Revision History

  • 2015-06-17
    Type: Non-polymer description | Details: update synonyms
  • 2012-08-01
    Type: Function and keywords | Details: update header, keywds
  • 2012-08-01
    Type: Other | Details: add remark900
  • 2012-07-18
    Type: Non-polymer description | Details: Update synonym for T27
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4