7RSX

HIV-1 gp120 complex with CJF-III-049-S

PDB DOI: https://doi.org/10.2210/pdb7RSX/pdb

Classification: VIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-08-12 Released: 2022-06-08
Deposition Author(s): Liang, S., Hendrickson, W.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.281
R-Value Work: 0.240
R-Value Observed: 0.242

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Identification of gp120 Residue His105 as a Novel Target for HIV-1 Neutralization by Small-Molecule CD4-Mimics.

Fritschi, C.J., Liang, S., Mohammadi, M., Anang, S., Moraca, F., Chen, J., Madani, N., Sodroski, J.G., Abrams, C.F., Hendrickson, W.A., Smith 3rd, A.B.

(2021) ACS Med Chem Lett 12: 1824-1831

PubMed: 34795873 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.1c00437
Primary Citation of Related Structures:
7RSX, 7RSY, 7RSZ

PubMed Abstract:
The design and synthesis of butyl chain derivatives at the indane ring 3-position of our lead CD4-mimetic compound BNM-III-170 that inhibits human immunodeficiency virus (HIV-1) infection are reported. Optimization efforts were guided by crystallographic and computational analysis of the small-molecule ligands of the Phe43 cavity of the envelope glycoprotein gp120. Biological evaluation of 11 - 21 revealed that members of this series of CD4-mimetic compounds are able to inhibit HIV-1 viral entry into target cells more potently and with greater breadth compared to BNM-III-170. Crystallographic analysis of the binding pocket of 14 , 16 , and 17 revealed a novel hydrogen bonding interaction between His105 and a primary hydroxyl group on the butyl side chain. Further optimization of this interaction with the His105 residue holds the promise of more potent CD4-mimetic compounds.

Organizational Affiliation

Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.

Macromolecule Content

Total Structure Weight: 169.15 kDa
Atom Count: 11,059
Modelled Residue Count: 1,340
Deposited Residue Count: 1,448
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENVELOPE GLYCOPROTEIN GP120	A [auth C], B, C [auth A], D	362	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain B Focus chain C [auth A] Focus chain D
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7IT (Subject of Investigation/LOI) Query on 7IT Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain J [auth C] SDF format, chain P [auth B] SDF format, chain W [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain J [auth C] MOL2 format, chain P [auth B] MOL2 format, chain W [auth A]	EA [auth D], J [auth C], P [auth B], W [auth A]	N~1~-{(1R,2R,3S)-2-(carbamimidamidomethyl)-3-[(3S)-3,4-dihydroxybutyl]-5-[(methylamino)methyl]-2,3-dihydro-1H-inden-1-yl}-N~2~-(4-chloro-3-fluorophenyl)ethanediamide C₂₅ H₃₂ Cl F N₆ O₄ FZJJRAXEHQBZEC-BXYJTDFISA-N		Interactions Focus chain EA [auth D] Focus chain J [auth C] Focus chain P [auth B] Focus chain W [auth A] Interactions & Density Focus chain EA [auth D] Focus chain J [auth C] Focus chain P [auth B] Focus chain W [auth A]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain E [auth C] SDF format, chain F [auth C] SDF format, chain FA [auth E] SDF format, chain G [auth C] SDF format, chain GA [auth E] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain FA [auth E] MOL2 format, chain G [auth C] MOL2 format, chain GA [auth E] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] E [auth C] AA [auth D], BA [auth D], CA [auth D], DA [auth D], E [auth C], F [auth C], FA [auth E], G [auth C], GA [auth E], H [auth C], I [auth C], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], X [auth D], Y [auth D], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth C] Focus chain F [auth C] Focus chain FA [auth E] Focus chain G [auth C] Focus chain GA [auth E] Focus chain H [auth C] Focus chain I [auth C] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth C] Focus chain F [auth C] Focus chain FA [auth E] Focus chain G [auth C] Focus chain GA [auth E] Focus chain H [auth C] Focus chain I [auth C] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]