4IBK

Ebola virus VP35 bound to small molecule

Structural Biology Knowledgebase: 4IBK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.192

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IBK

Classification: TRANSCRIPTION / TRANSCRIPTION inhibitor

Total Structure Weight: 29706.28

Macromolecule Entities
Molecule Chains Length Organism Details
Polymerase cofactor VP35 A, B 129 Zaire ebolavirus Fragment: unp residues 215-340
Gene Name(s): VP35
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1DE
Query on 1DE

A, B 3-{(2S)-2-(7-chloro-1,3-benzodioxol-5-yl)- 3-[(5-chlorothiophen-2-yl)carbonyl]-4-hydroxy- 5-oxo-2,5-dihydro-1H-pyrrol-1-yl}benzoic acid
C23 H13 Cl2 N O7 S
FYJSIGVCZLLXAT-SFHVURJKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1DE N/A in BindingDB
Kd: 50400 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.192
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 51.22 α = 90.00
b = 65.69 β = 90.00
c = 72.83 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-08
  • Released Date: 2014-03-19
  • Deposition author(s): Brown, C.S., Leung, D.W., Xu, W., Borek, D.M., Otwinowski, Z., Ramanan, P., Stubbs, A.J., Peterson, D.S., Binning, J.M., Amarasinghe, G.K.

Revision History

  • 2014-05-14
    Type: Citation | Details: Citation update