4RZ8 | pdb_00004rz8

Crystal structure of HIV-1 gp120 core in complex with NBD-11021, a small molecule CD4-antagonist

PDB DOI: https://doi.org/10.2210/pdb4RZ8/pdb

Classification: VIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2014-12-18 Released: 2015-09-09
Deposition Author(s): Kwon, Y.D., Debnath, A.K., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.243 (Depositor), 0.245 (DCC)
R-Value Work:
0.227 (Depositor), 0.229 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structure-Based Design of a Small Molecule CD4-Antagonist with Broad Spectrum Anti-HIV-1 Activity.

Curreli, F., Kwon, Y.D., Zhang, H., Scacalossi, D., Belov, D.S., Tikhonov, A.A., Andreev, I.A., Altieri, A., Kurkin, A.V., Kwong, P.D., Debnath, A.K.

(2015) J Med Chem 58: 6909-6927

PubMed: 26301736 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.5b00709
Primary Citation Related Structures:
4RZ8

PubMed Abstract:
Earlier we reported the discovery and design of NBD-556 and their analogs which demonstrated their potential as HIV-1 entry inhibitors. However, progress in developing these inhibitors has been stymied by their CD4-agonist properties, an unfavorable trait for use as drug. Here, we demonstrate the successful conversion of a full CD4-agonist (NBD-556) through a partial CD4-agonist (NBD-09027), to a full CD4-antagonist (NBD-11021) by structure-based modification of the critical oxalamide midregion, previously thought to be intolerant of modification. NBD-11021 showed unprecedented neutralization breath for this class of inhibitors, with pan-neutralization against a panel of 56 Env-pseudotyped HIV-1 representing diverse subtypes of clinical isolates (IC50 as low as 270 nM). The cocrystal structure of NBD-11021 complexed to a monomeric HIV-1 gp120 core revealed its detail binding characteristics. The study is expected to provide a framework for further development of NBD series as HIV-1 entry inhibitors for clinical application against AIDS.

Organizational Affiliation

Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, New York 10065, United States.

Macromolecule Content

Total Structure Weight: 168.22 kDa
Atom Count: 12,011
Modeled Residue Count: 1,351
Deposited Residue Count: 1,412
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A, B, C, D	353	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: env
UniProt
Find proteins for A0A0M3KKW9 (Human immunodeficiency virus type 1) Explore A0A0M3KKW9 Go to UniProtKB: A0A0M3KKW9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0M3KKW9
Glycosylation
Glycosylation Sites: 11	Glycosylation Focus chain A Focus chain B 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
3ZM Query on 3ZM Download:Ideal Coordinates CCD File SDF format, chain LA [auth C] SDF format, chain N [auth A] SDF format, chain Y [auth B] SDF format, chain YA [auth D] MOL2 format, chain LA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] mmCIF format, chain LA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D]	LA [auth C], N [auth A], Y [auth B], YA [auth D]	5-(4-chlorophenyl)-N-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2R)-piperidin-2-yl]methyl}-1H-pyrrole-2-carboxamide C₂₂ H₂₅ Cl N₄ O₂ S FITIBROTOQOZHT-XLIONFOSSA-N		Interactions Focus chain LA [auth C] Focus chain N [auth A] Focus chain Y [auth B] Focus chain YA [auth D] Interactions & Density Focus chain LA [auth C] Focus chain N [auth A] Focus chain Y [auth B] Focus chain YA [auth D]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain MA [auth C] SDF format, chain O [auth A] SDF format, chain ZA [auth D] SDF format, chain Z [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain ZA [auth D] MOL2 format, chain Z [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain ZA [auth D] mmCIF format, chain Z [auth B]	MA [auth C], O [auth A], Z [auth B], ZA [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain MA [auth C] Focus chain O [auth A] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain MA [auth C] Focus chain O [auth A] Focus chain Z [auth B] Focus chain ZA [auth D]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain P [auth B] SDF format, chain PA [auth D] SDF format, chain Q [auth B] SDF format, chain QA [auth D] SDF format, chain R [auth B] SDF format, chain RA [auth D] SDF format, chain S [auth B] SDF format, chain SA [auth D] SDF format, chain T [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain UA [auth D] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] E [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], M [auth A], NA [auth D], OA [auth D], P [auth B], PA [auth D], Q [auth B], QA [auth D], R [auth B], RA [auth D], S [auth B], SA [auth D], T [auth B], TA [auth D], U [auth B], UA [auth D], V [auth B], VA [auth D], W [auth B], WA [auth D], X [auth B], XA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.243 (Depositor), 0.245 (DCC)
R-Value Work: 0.227 (Depositor), 0.229 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.621	α = 90
b = 68.842	β = 110.59
c = 116.192	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
PROTEUM PLUS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-09-09

Deposition Author(s):

Kwon, Y.D.

Debnath, A.K.

Kwong, P.D.

Revision History (Full details and data files)

Version 1.0: 2015-09-09
Type: Initial release
Version 1.1: 2015-09-23
Changes: Database references
Version 1.2: 2017-08-02
Changes: Data collection, Refinement description, Source and taxonomy
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.5: 2024-10-16
Changes: Structure summary