4I53

Crystal structure of clade C1086 HIV-1 gp120 core in complex with DMJ-II-121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5002 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-Based Design and Synthesis of an HIV-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization.

Lalonde, J.M.Le-Khac, M.Jones, D.M.Courter, J.R.Park, J.Schon, A.Princiotto, A.M.Wu, X.Mascola, J.R.Freire, E.Sodroski, J.Madani, N.Hendrickson, W.A.Smith, A.B.

(2013) ACS Med Chem Lett 4: 338-343

  • DOI: 10.1021/ml300407y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The design, synthesis, thermodynamic and crystallographic characterization of a potent, broad spectrum, second-generation HIV-1 entry inhibitor that engages conserved carbonyl hydrogen bonds within gp120 has been achieved. The optimized antagonist ex ...

    The design, synthesis, thermodynamic and crystallographic characterization of a potent, broad spectrum, second-generation HIV-1 entry inhibitor that engages conserved carbonyl hydrogen bonds within gp120 has been achieved. The optimized antagonist exhibits a sub-micromolar binding affinity (110 nM) and inhibits viral entry of clade B and C viruses (IC50 geometric mean titer of 1.7 and 14.0 μM, respectively), without promoting CD4-independent viral entry. thermodynamic signatures indicate a binding preference for the (R,R)-over the (S,S)-enantiomer. The crystal structure of the small molecule-gp120 complex reveals the displacement of crystallographic water and the formation of a hydrogen bond with a backbone carbonyl of the bridging sheet. Thus, structure-based design and synthesis targeting the highly conserved and structurally characterized CD4:gp120 interface is an effective tactic to enhance the neutralization potency of small molecule HIV-1 entry inhibitors.


    Organizational Affiliation

    Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA 19010.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 glycoprotein
A, B
358Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for C6G099 (Human immunodeficiency virus 1)
Go to UniProtKB:  C6G099
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
1C1
Query on 1C1

Download SDF File 
Download CCD File 
A, B
amino({[(1R,2R)-1-({[(4-chloro-3-fluorophenyl)amino](oxo)acetyl}amino)-2,3-dihydro-1H-inden-2-yl]methyl}amino)methaniminium
[amino({[(1R,2R)-1-{[(4-chloro-3- fluorophenyl)carbamoyl]formamido}-2,3-dihydro-1H- inden-2-yl]methyl}amino)methylidene]azanium
C19 H20 Cl F N5 O2
PZYMVIYVOCOSHZ-BDJLRTHQSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1C1Kd: 110 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5002 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.254 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 67.450α = 90.00
b = 127.670β = 90.00
c = 192.900γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release