PDB-9n3h: Crystal structure of HBV capsid with compound 18

ID or keywords:

Entry

Database: PDB / ID: 9n3h

Title

Crystal structure of HBV capsid with compound 18

Components

Capsid protein

Keywords

VIRAL PROTEIN / HBV capsid

Function / homology

Function and homology information

microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / identical protein binding
Similarity search - Function

Biological species

Hepatitis B virus genotype D subtype adw

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.543 Å

Authors

White, A. / Lakshminarasimhan, D. / Cakici, O. / Suto, R.

Funding support

United States, 1items

Citation

Journal: Acs Med.Chem.Lett. / Year: 2025
Title: Discovery of VNRX-9945, a Potent, Broadly Active Capsid Assembly Modulator as a Clinical Candidate for the Treatment of Chronic Hepatitis B Virus Infection
Authors: Liu, B. / Yao, J. / Haimowitz, T. / Benetatos, C.A. / Boyd, S.A. / Condon, S.M. / Burns, C.J. / White, A. / Lakshminarasimhan, D. / Suto, R.K. / Cakici, O. / Drager, A.S. / Hart, S.G.E. / ...

History

Deposition	Jan 31, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 2, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9n3h.cif.gz	71.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9n3h.ent.gz		Display	PDB format
PDBx/mmJSON format	9n3h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n3/9n3h ftp://data.pdbj.org/pub/pdb/validation_reports/n3/9n3h	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#62 - Feb 2005 Major Histocompatibility Complex similarity (3) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: Capsid protein

B: Capsid protein

hetero molecules

36.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	88.152, 88.152, 290.557
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	155
Space group name H-M	H32

#1: Protein	Capsid protein / Core antigen / Core protein / HBcAg / p21.5 Mass: 18004.578 Da / Num. of mol.: 2 / Mutation: Y132A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979) Strain: isolate United Kingdom/adyw/1979 / Gene: C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03147
#2: Chemical	ChemComp-A1BVU / N-[3-(difluoromethyl)phenyl]-5-[{[(1s,4s)-4-hydroxycyclohexyl]amino}(oxo)acetyl]-1,2,4-trimethyl-1H-pyrrole-3-carboxamide Mass: 447.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₃H₂₇F₂N₃O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.02 Å³/Da / Density % sol: 59.23 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 13-18% (v/v) MPD, 280-310 mM trisodium citrate, and 100 mM Hepes pH 7.5. Protein:reservoir ratio of 2:1

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 21, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2.54→48.473 Å / Num. obs: 14719 / % possible obs: 99.8 % / Redundancy: 8.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.124 / R_pim(I) all: 0.044 / R_rim(I) all: 0.132 / Χ²: 0.92 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.54→2.66 Å / Redundancy: 8.3 % / R_merge(I) obs: 0.921 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1753 / CC_1/2: 0.924 / R_pim(I) all: 0.336 / R_rim(I) all: 0.982 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.543→48.473 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.924 / Cross valid method: FREE R-VALUE / ESU R: 0.438 / ESU R Free: 0.305
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2966	779	5.292 %
R_work	0.2605	13940	-
all	0.262	-	-
obs	-	14719	99.79 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 88.676 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.776 Å²	-4.388 Å²	0 Å²
2-	-	-8.776 Å²	0 Å²
3-	-	-	28.47 Å²

Refinement step

Cycle: LAST / Resolution: 2.543→48.473 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2118	0	64	6	2188

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	2251
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2071
X-RAY DIFFRACTION	r_angle_refined_deg	1.483	1.841	3089
X-RAY DIFFRACTION	r_angle_other_deg	0.799	1.75	4764
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.066	5	264
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.008	5	13
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.027	10	322
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.665	10	91
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	348
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2601
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	515
X-RAY DIFFRACTION	r_nbd_refined	0.251	0.2	588
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.221	0.2	1865
X-RAY DIFFRACTION	r_nbtor_refined	0.194	0.2	1106
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1068
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.225	0.2	52
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.154	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.134	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.21	0.2	43
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.168	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	6.59	8.927	1068
X-RAY DIFFRACTION	r_mcbond_other	6.584	8.928	1068
X-RAY DIFFRACTION	r_mcangle_it	10.568	16.001	1328
X-RAY DIFFRACTION	r_mcangle_other	10.568	16.001	1329
X-RAY DIFFRACTION	r_scbond_it	6.123	9.144	1183
X-RAY DIFFRACTION	r_scbond_other	6.121	9.147	1184
X-RAY DIFFRACTION	r_scangle_it	10.196	16.787	1761
X-RAY DIFFRACTION	r_scangle_other	10.193	16.788	1762
X-RAY DIFFRACTION	r_lrange_it	15.04	86.117	2643
X-RAY DIFFRACTION	r_lrange_other	15.051	86.083	2641

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.543-2.609	0.501	58	0.439	992	0.443	1061	0.234	0.379	98.9632	0.373
2.609-2.68	0.487	64	0.515	987	0.513	1052	0.407	0.352	99.9049	0.457
2.68-2.758	0.419	43	0.476	970	0.473	1013	0.497	0.343	100	0.412
2.758-2.842	0.458	43	0.434	938	0.435	983	0.482	0.381	99.7965	0.382
2.842-2.935	0.383	59	0.414	896	0.412	956	0.313	0.433	99.8954	0.356
2.935-3.038	0.34	51	0.419	884	0.415	935	0.527	0.472	100	0.375
3.038-3.152	0.398	42	0.402	841	0.402	888	0.517	0.499	99.4369	0.367
3.152-3.28	0.429	45	0.361	814	0.364	860	0.515	0.555	99.8837	0.338
3.28-3.425	0.276	42	0.322	787	0.32	830	0.782	0.701	99.8795	0.3
3.425-3.592	0.283	47	0.283	745	0.283	792	0.927	0.843	100	0.268
3.592-3.785	0.201	39	0.224	729	0.223	768	0.968	0.946	100	0.22
3.785-4.013	0.266	37	0.185	691	0.189	728	0.958	0.969	100	0.182
4.013-4.288	0.221	34	0.154	631	0.157	665	0.953	0.979	100	0.154
4.288-4.628	0.188	28	0.146	621	0.148	650	0.983	0.982	99.8462	0.151
4.628-5.065	0.22	38	0.168	545	0.172	584	0.969	0.977	99.8288	0.181
5.065-5.656	0.304	30	0.191	506	0.197	536	0.946	0.975	100	0.201
5.656-6.516	0.334	23	0.228	459	0.233	482	0.949	0.967	100	0.243
6.516-7.944	0.328	20	0.214	396	0.22	416	0.936	0.967	100	0.23
7.944-11.087	0.205	24	0.182	310	0.184	337	0.978	0.977	99.1098	0.217
11.087-48.473	0.445	12	0.248	198	0.258	210	0.819	0.959	100	0.291

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