6HS4

Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based in Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library.

Shaikh, F.Zhao, Y.Alvarez, L.Iliopoulou, M.Lohans, C.Schofield, C.J.Padilla-Parra, S.Siu, S.W.I.Fry, E.E.Ren, J.Stuart, D.I.

(2019) J.Med.Chem. 62: 2928-2937


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein,GP1,Envelope glycoprotein
A
331Zaire ebolavirus (strain Mayinga-76)Mutation(s): 1 
Gene Names: GP
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76))
Go to UniProtKB:  Q05320
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein
B
168Zaire ebolavirus (strain Mayinga-76)Mutation(s): 1 
Gene Names: GP
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76))
Go to UniProtKB:  Q05320
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GON
Query on GON

Download SDF File 
Download CCD File 
A
1-[2-[3-oxidanyl-4-(4-phenyl-1~{H}-pyrazol-5-yl)phenoxy]ethyl]piperidine-4-carboxamide
C23 H26 N4 O3
PYIQTHALSLWYHD-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 114.160α = 90.00
b = 114.160β = 90.00
c = 305.458γ = 120.00
Software Package:
Software NamePurpose
DIALSdata scaling
REFMACphasing
DIALSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-04-10
    Type: Data collection, Database references