9X7T | pdb_00009x7t

Dengue 3 NS5 methyltransferase bound to S-Adenosyl-L-homocysteine and Herbacetin

PDB DOI: https://doi.org/10.2210/pdb9X7T/pdb
Entry: 9X7T supersedes: 8ZMC

Classification: TRANSFERASE
Organism(s): dengue virus type 3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-10-17 Released: 2026-06-10
Deposition Author(s): Bhutkar, M., Verma, S., Tomar, S., Kumar, P.
Funding Organization(s): Department of Science & Technology (DST, India), Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.299 (Depositor), 0.300 (DCC)
R-Value Work:
0.222 (Depositor), 0.225 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Mechanistic Insights Into the Inhibition of Dengue Virus NS5 Methyltransferase by Herbacetin.

Bhutkar, M., Verma, S., Singh, V., Kumar, P., Tomar, S.

(2026) Proteins 94: 1115-1123

PubMed: 41431129 Search on PubMed
DOI: https://doi.org/10.1002/prot.70108
Primary Citation Related Structures:
9X7T

PubMed Abstract:
Herbacetin (HC) is a naturally occurring flavonoid compound with a dual antiviral mechanism. It inhibits the polyamine biosynthetic pathway and targets the methyltransferase (MTase) enzyme of both the dengue virus (DENV) and chikungunya virus (CHIKV). However, the detailed inhibition mechanism of DENV-3 non-structural protein (NS5) MTase by HC remains unclear. This study provides structural insights into the inhibition mechanism of HC by analyzing the crystal structure of DENV-3 NS5 MTase complexed with HC and S-adenosyl-L-homocysteine. Structural analysis revealed that HC binds to the Cap 0-RNA site near the GTP binding site in the DENV-3 NS5 MTase. Additionally, the fluorescence polarization assay demonstrated that HC inhibits GTP binding with an inhibition constant (K _i) value of ~0.43 μM. This is one of the first studies that identify an inhibitor that targets the conserved RNA-binding region of NS5 MTase, suggesting its potential as a highly effective scaffold for broad-spectrum antiviral agents against orthoflaviviruses.

Organizational Affiliation

Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India.

Macromolecule Content

Total Structure Weight: 65.84 kDa
Atom Count: 4,298
Modeled Residue Count: 512
Deposited Residue Count: 568
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS5 methyltransferase	A, B	284	dengue virus type 3	Mutation(s): 0
UniProt
Find proteins for C1KBQ3 (Dengue virus type 3) Explore C1KBQ3 Go to UniProtKB: C1KBQ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C1KBQ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
A1L1Z (Subject of Investigation/LOI) Query on A1L1Z Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	Herbacetin C₁₅ H₁₀ O₇ ZDOTZEDNGNPOEW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.299 (Depositor), 0.300 (DCC)
R-Value Work: 0.222 (Depositor), 0.225 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.966	α = 90
b = 185.044	β = 90
c = 50.877	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-10

Deposition Author(s):

This entry supersedes: 8ZMC

Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	CRG/2023/002214
Department of Biotechnology (DBT, India)	India	BT/PR40141/BTIS/137/16/2021
Department of Biotechnology (DBT, India)	India	BT/PR40142/BTIS/137/72/2023