7RSZ

HIV-1 gp120 complex with CJF-II-204

PDB DOI: https://doi.org/10.2210/pdb7RSZ/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: 2.79 Å
R-Value Free: 0.259
R-Value Work: 0.236
R-Value Observed: 0.237

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 171.29 kDa
Atom Count: 11,202
Modelled Residue Count: 1,340
Deposited Residue Count: 1,448
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 gp120 Clade C1086	A [auth B], B [auth A], C, 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 A [auth B] Focus chain B [auth A] Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7IT Query on 7IT Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain KA [auth D] SDF format, chain L [auth B] SDF format, chain U [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain U [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth B] mmCIF format, chain U [auth A]	CA [auth C], KA [auth D], L [auth B], U [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 CA [auth C] Focus chain KA [auth D] Focus chain L [auth B] Focus chain U [auth A]
7IW (Subject of Investigation/LOI) Query on 7IW Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain JA [auth D] SDF format, chain K [auth B] SDF format, chain T [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth B] MOL2 format, chain T [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth B] mmCIF format, chain T [auth A]	BA [auth C], JA [auth D], K [auth B], T [auth A]	N~1~-{(1R,2R,3S)-2-(carbamimidamidomethyl)-3-[(3R)-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-GDVTWYKTSA-N		Interactions Focus chain BA [auth C] Focus chain JA [auth D] Focus chain K [auth B] Focus chain T [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain DA [auth D] SDF format, chain E [auth B] SDF format, chain EA [auth D] SDF format, chain F [auth B] SDF format, chain FA [auth D] SDF format, chain G [auth B] SDF format, chain GA [auth D] SDF format, chain H [auth B] SDF format, chain HA [auth D] SDF format, chain I [auth B] SDF format, chain IA [auth D] SDF format, chain J [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth B] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth B] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth B] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth B] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth B] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth B] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth B] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] DA [auth D] E [auth B] EA [auth D] F [auth B] AA [auth C], DA [auth D], E [auth B], EA [auth D], F [auth B], FA [auth D], G [auth B], GA [auth D], H [auth B], HA [auth D], I [auth B], IA [auth D], J [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain DA [auth D] Focus chain E [auth B] Focus chain EA [auth D] Focus chain F [auth B] Focus chain FA [auth D] Focus chain G [auth B] Focus chain GA [auth D] Focus chain H [auth B] Focus chain HA [auth D] Focus chain I [auth B] Focus chain IA [auth D] Focus chain J [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]