3ZCM

Small molecule inhibitors of the LEDGF site of HIV integrase identified by fragment screening and structure based design.

Structural Biology Knowledgebase: 3ZCM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.164

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ZCM

Classification: TRANSFERASE

Total Structure Weight: 38647.70

Macromolecule Entities
Molecule Chains Length Organism Details
HIV INTEGRASE A, B 167 Human immunodeficiency virus EC#: 2.7.7 IUBMB
Fragment: CORE CATALYTIC DOMAIN, RESIDUES 56-212
Mutation: C56S, F139D, F185H
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PX3
Query on PX3

A, B 5-[[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl- prop-2-enyl-amino]methyl]-1,3-benzodioxole- 4-carboxylic acid
C28 H28 N2 O6
WRLIFDLBMCTVHJ-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)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PX3 N/A in BindingDB
Kd: 519000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.164
  • Space Group: P 31
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.86 α = 90.00
b = 70.86 β = 90.00
c = 67.13 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-21
  • Released Date: 2012-12-05
  • Deposition author(s): Peat, T.S.

Revision History

No revisions since initial release