PDB-4tyd: Structure-based design of a novel series of azetidine inhibitors ...

ID or keywords:

Entry

Database: PDB / ID: 4tyd

Title

Structure-based design of a novel series of azetidine inhibitors of the hepatitis C virus NS3/4A serine protease

Components

NS3 protease

Keywords

HYDROLASE / Structure-based design / HCV NS3/4A serine protease / azetidine inhibitors / PROTEROS BIOSTRUCTURES GMBH

Function / homology

Function and homology information

transformation of host cell by virus / host cell membrane / serine-type peptidase activity /

virion component / symbiont entry into host cell / virion attachment to host cell /

proteolysis /

membrane /

metal ion binding
Similarity search - Function

Biological species

Hepatitis C virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.84 Å

Authors

Parsy, C.

Citation

Journal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: Structure-based design of a novel series of azetidine inhibitors of the hepatitis C virus NS3/4A serine protease.
Authors: Parsy, C. / Alexandre, F.R. / Brandt, G. / Caillet, C. / Cappelle, S. / Chaves, D. / Convard, T. / Derock, M. / Gloux, D. / Griffon, Y. / Lallos, L. / Leroy, F. / Liuzzi, M. / Loi, A.G. / ...

History

Deposition	Jul 8, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Sep 10, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 24, 2014	Group: Database references
Revision 1.2	Apr 25, 2018	Group: Data collection / Category: reflns / reflns_shell Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.3	May 8, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4tyd.cif.gz	878.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4tyd.ent.gz	741 KB	Display	PDB format
PDBx/mmJSON format	4tyd.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/ty/4tyd ftp://data.pdbj.org/pub/pdb/validation_reports/ty/4tyd	HTTPS FTP

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Related structure data

Similar structure data	3lb8-2 3r1b-4 3r1b-2 5mu3-2 1o96-2 4pqp-d 4i2s-d 2rde-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (3)

Deposited unit

A: NS3 protease

B: NS3 protease

C: NS3 protease

D: NS3 protease

E: NS3 protease

F: NS3 protease

G: NS3 protease

H: NS3 protease

J: NS3 protease

K: NS3 protease

L: NS3 protease

M: NS3 protease

hetero molecules

268 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NS3 protease

D: NS3 protease

F: NS3 protease

hetero molecules

defined by software
67 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: NS3 protease

C: NS3 protease

E: NS3 protease

hetero molecules

defined by software
67 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: NS3 protease

H: NS3 protease

M: NS3 protease

hetero molecules

defined by software
66.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: NS3 protease

K: NS3 protease

L: NS3 protease

hetero molecules

defined by software
66.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	140.691, 143.197, 240.550
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	NS3 protease Mass: 21461.828 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus (isolate 1) / Production host: Escherichia coli (E. coli) / References: UniProt: Q0ZNA6
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-3EO / (4R,6S,7Z,15S,17S)-17-[({7-methoxy-2-[4-(propan-2-yl)-1,3-thiazol-2-yl]quinolin-4-yl}oxy)methyl]-13-methyl-N-[(1-methylcyclopropyl)sulfonyl]-2,14-dioxo-1,3,13-triazatricyclo[13.2.0.0~4,6~]heptadec-7-ene-4-carboxamide Mass: 750.927 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃₇H₄₆N₆O₇S₂
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.39 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.919 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.919 Å / Relative weight: 1
Reflection	Resolution: 2.84→49.15 Å / Num. obs: 57364 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / R_merge(I) obs: 0.133
Reflection shell	Resolution: 2.84→2.91 Å / Redundancy: 7.8 % / R_merge(I) obs: 0.793 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.84→49.15 Å / Cor.coef. F_o:F_c: 0.924 / Cor.coef. F_o:F_c free: 0.896 / SU B: 41.754 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26657	997	1.7 %	RANDOM
R_work	0.22088	-	-	-
obs	0.22167	56366	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 71.324 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2 Å²	0 Å²	0 Å²
2-	-	-1.07 Å²	0 Å²
3-	-	-	1.27 Å²

Refinement step

Cycle: 1 / Resolution: 2.84→49.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17038	0	647	1	17686

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	18044
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	16881
X-RAY DIFFRACTION	r_angle_refined_deg	1.105	2.016	24701
X-RAY DIFFRACTION	r_angle_other_deg	0.918	3	39054
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.952	5	2297
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.245	21.652	587
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.151	15	2758
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.91	15	167
X-RAY DIFFRACTION	r_chiral_restr	0.056	0.2	2867
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	19766
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3521
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	3460
X-RAY DIFFRACTION	r_nbd_other	0.168	0.2	17365
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	8866
X-RAY DIFFRACTION	r_nbtor_other	0.08	0.2	10917
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	474
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.139	0.2	41
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.171	0.2	144
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.162	0.2	5
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.324	2	14682
X-RAY DIFFRACTION	r_mcbond_other	0.044	2	4790
X-RAY DIFFRACTION	r_mcangle_it	0.415	3	18521
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.616	4	7757
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.989	6	6012
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.84→2.914 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.318	72	-
R_work	0.319	4112	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	9.3484	-0.7413	2.658	3.9784	-0.1781	4.9537	0.0363	-0.8768	-0.0832	0.459	-0.2679	0.1833	0.3719	-0.3222	0.2316	0.042	-0.3058	0.1277	-0.1575	-0.078	-0.3943	48.571	-20.143	43.547
2	5.1804	-1.746	0.8594	3.7649	-1.3175	2.627	0.0975	-0.3418	0.1421	0.5882	-0.1475	-0.3722	0.2051	0.3857	0.05	0.0685	-0.2167	-0.0063	-0.1253	0.0662	-0.3689	62.439	-25.48	40.521
3	4.0447	-0.4927	-1.5667	5.4985	-0.4926	6.7833	-0.0535	0.0313	0.6675	0.1182	0.2692	-0.3632	-0.2367	0.3424	-0.2158	-0.2528	-0.0563	-0.027	-0.2639	-0.0522	-0.2486	18.292	4.093	32.331
4	6.2138	-0.0781	-0.192	5.7951	-0.3101	0.7457	-0.2296	-0.2474	0.6955	0.1918	0.1994	0.4955	-0.3425	-0.3254	0.0303	-0.2139	0.0301	-0.0328	-0.1941	-0.031	-0.2067	3.401	5.235	29.685
5	4.5262	-0.6932	0.9997	3.0885	-0.3988	4.874	-0.3134	0.5969	-0.2837	-0.3162	0.1141	-0.0655	0.2874	0.1098	0.1993	-0.0044	-0.1804	0.1406	-0.1364	-0.1171	-0.452	16.839	-18.006	10.721
6	4.9227	0.2045	0.5475	3.0962	0.4428	2.1894	-0.1919	0.5928	-0.0034	-0.5455	0.1779	0.5057	0.1726	-0.2694	0.0141	-0.0429	-0.1538	0.0909	-0.1007	-0.1196	-0.2155	2.124	-21.306	12.308
7	4.8483	0.7562	-0.5357	3.1673	-0.3868	4.7741	0.0882	0.1411	1.0011	0.2345	-0.3216	0.0749	-0.4916	-0.135	0.2335	-0.2269	-0.0472	0.0792	-0.1644	0.0465	-0.0351	47.543	0.79	20.932
8	5.3174	0.834	-0.4622	4.9853	-0.1288	2.2363	0.078	0.3378	0.9227	-0.2923	-0.11	-0.3593	-0.2498	0.3625	0.0321	-0.2204	-0.148	0.0951	-0.0871	0.0424	-0.0623	62.662	-0.13	21.651
9	4.6072	2.0457	-1.2547	5.347	-1.708	7.0989	-0.2187	-0.6898	-0.906	-0.0122	-0.6	-0.8657	0.7683	0.8989	0.8187	-0.3527	0.152	0.2019	-0.0217	0.2665	0.0778	17.973	-25.75	40.776
10	3.8076	2.6691	-0.701	3.0244	-2.8837	8.14	-0.088	-0.0945	-0.4928	-0.248	-0.2399	-0.0801	0.8928	-0.2287	0.3278	-0.3083	0.0256	0.1145	-0.1092	-0.0213	-0.2833	3.343	-22.972	43.644
11	6.6846	-0.866	-0.0343	6.2125	-0.3184	4.1214	0.2562	0.6307	-0.4669	-0.0584	-0.0827	0.3836	0.7017	0.0973	-0.1735	-0.1035	-0.0339	-0.0007	-0.1988	-0.1173	-0.3199	42.893	-29.608	14.336
12	5.9859	-1.0367	0.2545	3.0909	1.2644	3.0413	0.4686	0.7783	-0.734	-0.2291	-0.4434	-0.1012	0.7747	0.5178	-0.0252	0.0466	0.1663	0.0155	0.175	-0.0562	-0.3579	57.244	-28.875	9.488
13	5.8568	-0.8534	0.0829	6.8414	-1.2624	6.1556	0.1924	0.7442	0.477	-0.4572	-0.1197	-0.0351	-0.3597	-0.33	-0.0726	-0.2558	0.1219	-0.0604	-0.1679	-0.0005	-0.3561	16.738	45.107	20.207
14	2.7467	-0.8344	0.1777	8.5445	0.0529	3.8901	0.2307	0.796	-0.8252	-0.4784	-0.287	0.2898	0.136	-0.5227	0.0562	-0.1509	0.0525	-0.0967	-0.0254	-0.1908	-0.2717	20.444	30.558	18.061
15	4.6353	-0.8006	-1.7102	5.0385	-0.6071	4.5915	0.3284	0.0168	0.0701	0.379	-0.5641	-1.0414	-0.785	0.7303	0.2356	-0.1642	-0.185	-0.1283	-0.1103	0.1121	0.075	46.032	47.298	29.459
16	5.8572	0.6023	0.1955	4.9726	-0.7652	3.5766	-0.0179	0.0472	-0.8434	-0.164	-0.556	-1.3884	0.2018	0.9926	0.574	-0.2116	-0.0153	-0.235	-0.0845	0.1992	0.3951	48.026	32.762	33.292
17	5.9466	1.7157	1.4413	4.7543	-1.8942	5.2699	0.0849	-0.9266	0.5795	0.6819	-0.0327	0.5688	-0.8283	-0.0767	-0.0521	0.2337	-0.0844	-0.1622	-0.1494	-0.0942	-0.2306	23.259	45.984	50.899
18	3.8508	0.7812	-1.0365	4.4026	-0.4591	7.0935	0.0202	-0.7288	-0.7536	0.8406	-0.1256	-0.4827	0.1228	0.1943	0.1055	-0.0032	-0.0902	-0.1689	-0.1931	0.1155	-0.2059	21.041	31.022	49.814
19	4.6798	0.3795	0.3124	5.0757	-0.0791	6.9278	0.3262	0.4831	0.136	-0.1272	-0.0943	0.5324	0.6185	-0.6274	-0.2319	-0.0054	0.0278	-0.0502	-0.2281	0.0185	-0.1486	27.302	2.872	79.568
20	5.746	-1.3367	-0.6115	4.1345	0.2667	2.501	0.2902	0.3651	0.9615	-0.3232	-0.1272	0.1148	-0.2853	-0.4847	-0.163	-0.0817	0.0801	0.1718	-0.2357	0.0347	0.2202	25.952	17.598	82.922
21	6.1913	0.2126	-2.0623	5.5873	0.5564	4.3949	-0.0121	-1.2675	0.0248	0.4855	0.1254	-0.1969	0.4263	0.597	-0.1132	-0.1126	0.0494	0.0852	0.1107	-0.0979	-0.0233	45.364	2.702	104.84
22	5.0911	1.086	0.2228	3.6831	0.7991	5.1565	0.4798	-1.2099	1.0044	0.3933	0.0673	-0.1522	-0.2268	0.4018	-0.547	-0.1081	-0.016	0.1292	0.1337	-0.3577	0.3492	49.409	17.308	104.303
23	6.876	0.494	-0.0186	4.3192	-0.4942	5.1745	0.2469	0.4612	0.0896	-1.036	-0.1621	-0.8453	0.3938	0.6217	-0.0847	0.0796	0.2456	0.2734	-0.1048	0.0601	0.1062	58.108	2.474	76.026
24	3.652	0.4036	-2.0281	7.3752	-2.4806	3.943	0.2628	0.2489	1.0696	-0.1774	-0.1644	-0.867	-0.3176	0.7893	-0.0985	0.178	0.0995	0.3107	0.0462	0.0796	0.3605	56.01	17.181	72.979

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 94
2	X-RAY DIFFRACTION	2	A	95 - 232
3	X-RAY DIFFRACTION	3	B	1 - 94
4	X-RAY DIFFRACTION	4	B	95 - 234
5	X-RAY DIFFRACTION	5	C	1 - 94
6	X-RAY DIFFRACTION	6	C	95 - 232
7	X-RAY DIFFRACTION	7	D	2 - 94
8	X-RAY DIFFRACTION	8	D	95 - 232
9	X-RAY DIFFRACTION	9	E	1 - 94
10	X-RAY DIFFRACTION	10	E	95 - 232
11	X-RAY DIFFRACTION	11	F	1 - 94
12	X-RAY DIFFRACTION	12	F	95 - 232
13	X-RAY DIFFRACTION	13	G	1 - 94
14	X-RAY DIFFRACTION	14	G	95 - 232
15	X-RAY DIFFRACTION	15	H	1 - 94
16	X-RAY DIFFRACTION	16	H	95 - 232
17	X-RAY DIFFRACTION	17	M	1 - 94
18	X-RAY DIFFRACTION	18	M	95 - 232
19	X-RAY DIFFRACTION	19	J	1 - 94
20	X-RAY DIFFRACTION	20	J	95 - 234
21	X-RAY DIFFRACTION	21	K	1 - 94
22	X-RAY DIFFRACTION	22	K	95 - 232
23	X-RAY DIFFRACTION	23	L	1 - 94
24	X-RAY DIFFRACTION	24	L	95 - 232

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