3OVN

Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase

Structural Biology Knowledgebase: 3OVN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.211

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3OVN

Classification: VIRAL PROTEIN / TRANSFERASE INHIBITOR

Total Structure Weight: 36947.18

Macromolecule Entities
Molecule Chains Length Organism Details
POL polyprotein A, B 163 Human immunodeficiency virus 1 Fragment: Integrase CATALYTIC CORE DOMAIN, 765-927
Mutation: C56S, W131D, F139D, F185H
Gene Name(s): pol

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SUC
Query on SUC

B SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPV
Query on MPV

A, B 1-methyl-3-(thiophen-2-yl)-1H-pyrazol-5-amine
C8 H9 N3 S
NFTITKUYTQZKIZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

A, B CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MPV N/A in BindingDB
Kd: 2800000 nM  BindingMOAD
Kd: 2800000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.211
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 59.75 α = 90.00
b = 59.70 β = 90.00
c = 81.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-09-16
  • Released Date: 2011-03-09
  • Deposition author(s): Wielens, J., Chalmers, D.K., Headey, S.J., Deadman, J.J., Rhodes, D.K., Parker, M.W., Scanlon, M.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4