6OOO | pdb_00006ooo

Crystal structure of HIV-1 LM/HT Clade A/E CRF01 gp120 core in complex with (S)-MCG-IV-226.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.275 (Depositor), 0.297 (DCC) 
  • R-Value Work: 
    0.216 (Depositor) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Optimization of Small Molecules That Sensitize HIV-1 Infected Cells to Antibody-Dependent Cellular Cytotoxicity.

Grenier, M.C.Ding, S.Vezina, D.Chapleau, J.P.Tolbert, W.D.Sherburn, R.Schon, A.Somisetti, S.Abrams, C.F.Pazgier, M.Finzi, A.Smith 3rd, A.B.

(2020) ACS Med Chem Lett 11: 371-378

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00445
  • Primary Citation Related Structures: 
    6OOO

  • PubMed Abstract: 

    With approximately 37 million people living with HIV worldwide and an estimated 2 million new infections reported each year, the need to derive novel strategies aimed at eradicating HIV-1 infection remains a critical worldwide challenge. One potential strategy would involve eliminating infected cells via antibody-dependent cellular cytotoxicity (ADCC). HIV-1 has evolved sophisticated mechanisms to conceal epitopes located in its envelope glycoprotein (Env) that are recognized by ADCC-mediating antibodies present in sera from HIV-1 infected individuals. Our aim is to circumvent this evasion via the development of small molecules that expose relevant anti-Env epitopes and sensitize HIV-1 infected cells to ADCC. Rapid elaboration of an initial screening hit using parallel synthesis and structure-based optimization has led to the development of potent small molecules that elicit this humoral response. Efforts to increase the ADCC activity of this class of small molecules with the aim of increasing their therapeutic potential was based on our recent cocrystal structures with gp120 core.


  • Organizational Affiliation
    • Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.

Macromolecule Content 

  • Total Structure Weight: 42.27 kDa 
  • Atom Count: 2,926 
  • Modeled Residue Count: 340 
  • Deposited Residue Count: 355 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 LM/HT Clade A/E CRF01 gp120355Human immunodeficiency virus 1Mutation(s): 7 
Gene Names: HIV-1 Env
UniProt
Find proteins for A0A0M3KKW9 (Human immunodeficiency virus type 1)
Explore A0A0M3KKW9 
Go to UniProtKB:  A0A0M3KKW9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KKW9
Glycosylation
Glycosylation Sites: 10
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MXJ
(Subject of Investigation/LOI)

Query on MXJ



Download:Ideal Coordinates CCD File
L [auth A](3S,5R)-5-amino-N~3~-(4-chloro-3-fluorophenyl)-N~1~-propylpiperidine-1,3-dicarboxamide
C16 H22 Cl F N4 O2
HYGODLCYAHQHCD-WDEREUQCSA-N
EPE

Query on EPE



Download:Ideal Coordinates CCD File
M [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
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [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: 2.40 Å
  • R-Value Free:  0.275 (Depositor), 0.297 (DCC) 
  • R-Value Work:  0.216 (Depositor) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.37α = 90
b = 66.85β = 90
c = 85.39γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI116274
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01AI120756
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI129769

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-13
    Changes: Structure summary