4DKR | pdb_00004dkr

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-169


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.208 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0LJClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

This is version 1.6 of the entry. See complete history


Literature

Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule HIV-1 Entry Inhibitors.

Lalonde, J.M.Kwon, Y.D.Jones, D.M.Sun, A.W.Courter, J.R.Soeta, T.Kobayashi, T.Princiotto, A.M.Wu, X.Schon, A.Freire, E.Kwong, P.D.Mascola, J.R.Sodroski, J.Madani, N.Smith, A.B.

(2012) J Med Chem 55: 4382-4396

  • DOI: https://doi.org/10.1021/jm300265j
  • Primary Citation of Related Structures:  
    4DKO, 4DKP, 4DKQ, 4DKR

  • PubMed Abstract: 

    Cellular infection by HIV-1 is initiated with a binding event between the viral envelope glycoprotein gp120 and the cellular receptor protein CD4. The CD4-gp120 interface is dominated by two hotspots: a hydrophobic gp120 cavity capped by Phe43(CD4) and an electrostatic interaction between residues Arg59(CD4) and Asp368(gp120). The CD4 mimetic small-molecule NBD-556 (1) binds within the gp120 cavity; however, 1 and related congeners demonstrate limited viral neutralization breadth. Herein, we report the design, synthesis, characterization, and X-ray structures of gp120 in complex with small molecules that simultaneously engage both binding hotspots. The compounds specifically inhibit viral infection of 42 tier 2 clades B and C viruses and are shown to be antagonists of entry into CD4-negative cells. Dual hotspot design thus provides both a means to enhance neutralization potency of HIV-1 entry inhibitors and a novel structural paradigm for inhibiting the CD4-gp120 protein-protein interaction.


  • Organizational Affiliation

    Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, USA. jlalonde@brynmawr.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 gp120 coreA,
B [auth C]
353Human immunodeficiency virus type 1 (BRU ISOLATE)Mutation(s): 0 
Gene Names: HIV-1 Env
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus type 1)
Explore Q0ED31 
Go to UniProtKB:  Q0ED31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ED31
Glycosylation
Glycosylation Sites: 11
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0LJ
Query on 0LJ

Download Ideal Coordinates CCD File 
BA [auth C],
O [auth A]
N-[(1R,2R)-2-carbamimidamido-2,3-dihydro-1H-inden-1-yl]-N'-(4-chloro-3-fluorophenyl)ethanediamide
C18 H17 Cl F N5 O2
ICNIHLCRBSFIFO-HUUCEWRRSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
AA [auth C],
N [auth A]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.208 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.443α = 90
b = 68.602β = 91.38
c = 94.542γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0LJClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2012-05-09
    Changes: Source and taxonomy
  • Version 1.2: 2012-06-20
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2021-05-19
    Changes: Source and taxonomy, Structure summary
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Refinement description
  • Version 1.6: 2024-10-30
    Changes: Structure summary