PDB-2zec: Potent, Nonpeptide Inhibitors of Human Mast Cell Tryptase

ID or keywords:

Entry

Database: PDB / ID: 2zec

Title

Potent, Nonpeptide Inhibitors of Human Mast Cell Tryptase

Components

Tryptase beta 2

Keywords

HYDROLASE / tryptase / serine protease

Function / homology

Function and homology information

tryptase / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / serine-type peptidase activity / defense response / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / identical protein binding
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.059 Å

Authors

Spurlino, J.C. / Lewandowski, F. / Milligan, C.

Citation

Journal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Potent, nonpeptide inhibitors of human mast cell tryptase. Synthesis and biological evaluation of novel spirocyclic piperidine amide derivatives
Authors: Costanzo, M.J. / Yabut, S.C. / Zhang, H.-C. / White, K.B. / de Garavilla, L. / Wang, Y. / Minor, L.K. / Tounge, B.A. / Barnakov, A.N. / Lewandowski, F. / Milligan, C. / Spurlino, J.C. / ...

History

Deposition	Dec 8, 2007	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 9, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 11, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2zec.cif.gz	208.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2zec.ent.gz	175.1 KB	Display	PDB format
PDBx/mmJSON format	2zec.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2zec_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	2zec_full_validation.pdf.gz	1.4 MB	Display
Data in XML	2zec_validation.xml.gz	45.2 KB	Display
Data in CIF	2zec_validation.cif.gz	62.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ze/2zec ftp://data.pdbj.org/pub/pdb/validation_reports/ze/2zec	HTTPS FTP

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Related structure data

Related structure data	2za5C 2zebC C: citing same article (ref.)
Similar structure data	2zeb-d 2bm2-d 2gdd-d 2fpz-d 2fww-d 4mqa-1 4a6l-d 5wi6-d 2f9o-d 2za5-d Search similar-shape structures by Omokage search (details) 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	#237 - Sep 2019 Nanodiscs and HDL similarity (1)

Deposited unit

A: Tryptase beta 2

B: Tryptase beta 2

C: Tryptase beta 2

D: Tryptase beta 2

hetero molecules

110 kDa, 4 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)	82.260, 82.260, 170.650
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	76
Space group name H-M	P4₁

#1: Protein	Tryptase beta 2 Mass: 27265.131 Da / Num. of mol.: 4 / Fragment: UNP residues 31-273 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TPSB2 References: UniProt: Q6B052, UniProt: Q15661*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical	ChemComp-11N / 1-[1'-(3-phenylacryloyl)spiro[1-benzofuran-3,4'-piperidin]-5-yl]methanamine Mass: 348.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₂H₂₄N₂O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.65 Å³/Da / Density % sol: 53.53 %

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→41.13 Å / Num. obs: 63811

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX		refinement
PDB_EXTRACT	3.004	data extraction

Refinement

Resolution: 2.059→41.13 Å / FOM work R set: 0.792 / Stereochemistry target values: ml

	R_factor	Num. reflection	% reflection
R_free	0.256	3192	5 %
R_work	0.207	-	-
obs	-	63811	91.31 %

Solvent computation

B_sol: 47.548 Å² / k_sol: 0.349 e/Å³

Displacement parameters

B_iso max: 83.66 Å² / B_iso mean: 28 Å² / B_iso min: 9.63 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.145 Å²	-0 Å²	0 Å²
2-	-	-1.145 Å²	-0 Å²
3-	-	-	2.291 Å²

Refinement step

Cycle: LAST / Resolution: 2.059→41.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7648	0	104	561	8313

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	0.632	1
X-RAY DIFFRACTION	f_bond_d	0.004	1
X-RAY DIFFRACTION	f_chiral_restr	0.048	1
X-RAY DIFFRACTION	f_dihedral_angle_d	13.616	1
X-RAY DIFFRACTION	f_plane_restr	0.003	1
X-RAY DIFFRACTION	f_nbd_refined	4.082	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.059-2.065	0.436	371	X-RAY DIFFRACTION	121	66
2.065-2.07	0.413	458	X-RAY DIFFRACTION	121	84
2.07-2.076	0.41	506	X-RAY DIFFRACTION	121	86
2.076-2.082	0.392	391	X-RAY DIFFRACTION	121	67
2.082-2.088	0.371	214	X-RAY DIFFRACTION	121	36
2.088-2.094	0.333	218	X-RAY DIFFRACTION	121	41
2.094-2.1	0.35	289	X-RAY DIFFRACTION	121	48
2.1-2.106	0.313	396	X-RAY DIFFRACTION	121	65
2.106-2.113	0.311	462	X-RAY DIFFRACTION	121	79
2.113-2.119	0.31	442	X-RAY DIFFRACTION	121	82
2.119-2.125	0.273	471	X-RAY DIFFRACTION	121	84
2.125-2.132	0.239	502	X-RAY DIFFRACTION	121	86
2.132-2.138	0.246	485	X-RAY DIFFRACTION	121	88
2.138-2.145	0.24	525	X-RAY DIFFRACTION	121	89
2.145-2.152	0.236	531	X-RAY DIFFRACTION	121	88
2.152-2.158	0.233	501	X-RAY DIFFRACTION	121	87
2.158-2.165	0.234	534	X-RAY DIFFRACTION	121	89
2.165-2.172	0.246	488	X-RAY DIFFRACTION	121	90
2.172-2.179	0.239	512	X-RAY DIFFRACTION	121	90
2.179-2.187	0.212	513	X-RAY DIFFRACTION	121	91
2.187-2.194	0.22	557	X-RAY DIFFRACTION	121	89
2.194-2.201	0.237	489	X-RAY DIFFRACTION	121	88
2.201-2.209	0.231	465	X-RAY DIFFRACTION	121	83
2.209-2.216	0.258	402	X-RAY DIFFRACTION	121	66
2.216-2.224	0.269	330	X-RAY DIFFRACTION	121	57
2.224-2.232	0.269	286	X-RAY DIFFRACTION	121	53
2.232-2.24	0.251	410	X-RAY DIFFRACTION	121	66
2.24-2.248	0.264	450	X-RAY DIFFRACTION	121	84
2.248-2.256	0.198	428	X-RAY DIFFRACTION	121	77
2.256-2.264	0.293	494	X-RAY DIFFRACTION	121	82
2.264-2.272	0.233	342	X-RAY DIFFRACTION	121	57
2.272-2.281	0.234	336	X-RAY DIFFRACTION	121	56
2.281-2.289	0.235	376	X-RAY DIFFRACTION	121	70
2.289-2.298	0.22	463	X-RAY DIFFRACTION	121	80
2.298-2.307	0.212	492	X-RAY DIFFRACTION	121	87
2.307-2.316	0.207	519	X-RAY DIFFRACTION	121	91
2.316-2.325	0.194	536	X-RAY DIFFRACTION	121	89
2.325-2.334	0.206	517	X-RAY DIFFRACTION	121	92
2.334-2.344	0.2	552	X-RAY DIFFRACTION	121	91
2.344-2.353	0.197	512	X-RAY DIFFRACTION	121	91
2.353-2.363	0.188	505	X-RAY DIFFRACTION	121	90
2.363-2.373	0.186	534	X-RAY DIFFRACTION	121	90
2.373-2.383	0.21	480	X-RAY DIFFRACTION	121	89
2.383-2.394	0.202	566	X-RAY DIFFRACTION	121	91
2.394-2.404	0.2	495	X-RAY DIFFRACTION	121	90
2.404-2.415	0.191	525	X-RAY DIFFRACTION	121	91
2.415-2.425	0.197	548	X-RAY DIFFRACTION	121	91
2.425-2.437	0.203	506	X-RAY DIFFRACTION	121	91
2.437-2.448	0.207	491	X-RAY DIFFRACTION	121	88
2.448-2.459	0.206	529	X-RAY DIFFRACTION	121	89
2.459-2.471	0.205	532	X-RAY DIFFRACTION	121	91
2.471-2.483	0.206	526	X-RAY DIFFRACTION	121	90
2.483-2.495	0.194	531	X-RAY DIFFRACTION	121	92
2.495-2.507	0.204	511	X-RAY DIFFRACTION	121	90
2.507-2.52	0.215	516	X-RAY DIFFRACTION	121	89
2.52-2.533	0.209	506	X-RAY DIFFRACTION	121	91
2.533-2.546	0.211	511	X-RAY DIFFRACTION	121	89
2.546-2.559	0.206	540	X-RAY DIFFRACTION	121	90
2.559-2.573	0.211	532	X-RAY DIFFRACTION	121	93
2.573-2.587	0.208	517	X-RAY DIFFRACTION	121	90
2.587-2.601	0.212	502	X-RAY DIFFRACTION	121	89
2.601-2.616	0.205	498	X-RAY DIFFRACTION	121	88
2.616-2.631	0.211	479	X-RAY DIFFRACTION	121	82
2.631-2.646	0.221	495	X-RAY DIFFRACTION	121	84
2.646-2.661	0.223	510	X-RAY DIFFRACTION	121	91
2.661-2.678	0.198	506	X-RAY DIFFRACTION	121	89
2.678-2.694	0.195	526	X-RAY DIFFRACTION	121	88
2.694-2.711	0.201	485	X-RAY DIFFRACTION	121	84
2.711-2.728	0.201	528	X-RAY DIFFRACTION	121	88
2.728-2.746	0.202	514	X-RAY DIFFRACTION	121	89
2.746-2.764	0.198	504	X-RAY DIFFRACTION	121	92
2.764-2.783	0.202	509	X-RAY DIFFRACTION	121	89
2.783-2.802	0.206	525	X-RAY DIFFRACTION	121	91
2.802-2.822	0.21	552	X-RAY DIFFRACTION	121	93
2.822-2.842	0.188	544	X-RAY DIFFRACTION	121	92
2.842-2.863	0.209	504	X-RAY DIFFRACTION	121	91
2.863-2.884	0.203	551	X-RAY DIFFRACTION	121	93
2.884-2.906	0.213	540	X-RAY DIFFRACTION	121	93
2.906-2.929	0.197	539	X-RAY DIFFRACTION	121	93
2.929-2.953	0.208	527	X-RAY DIFFRACTION	121	92
2.953-2.977	0.218	532	X-RAY DIFFRACTION	121	94
2.977-3.003	0.201	554	X-RAY DIFFRACTION	121	94
3.003-3.029	0.199	531	X-RAY DIFFRACTION	121	92
3.029-3.056	0.193	580	X-RAY DIFFRACTION	121	93
3.056-3.084	0.202	502	X-RAY DIFFRACTION	121	95
3.084-3.113	0.197	539	X-RAY DIFFRACTION	121	94
3.113-3.143	0.199	565	X-RAY DIFFRACTION	121	96
3.143-3.174	0.203	531	X-RAY DIFFRACTION	121	92
3.174-3.207	0.179	527	X-RAY DIFFRACTION	121	93
3.207-3.241	0.185	537	X-RAY DIFFRACTION	121	94
3.241-3.277	0.187	550	X-RAY DIFFRACTION	121	92
3.277-3.314	0.179	523	X-RAY DIFFRACTION	121	93
3.314-3.353	0.175	537	X-RAY DIFFRACTION	121	93
3.353-3.394	0.167	529	X-RAY DIFFRACTION	121	92
3.394-3.437	0.176	566	X-RAY DIFFRACTION	121	93
3.437-3.482	0.183	515	X-RAY DIFFRACTION	121	93
3.482-3.53	0.164	558	X-RAY DIFFRACTION	121	94
3.53-3.58	0.175	537	X-RAY DIFFRACTION	121	93
3.58-3.634	0.168	530	X-RAY DIFFRACTION	121	93
3.634-3.69	0.174	530	X-RAY DIFFRACTION	121	92
3.69-3.751	0.167	574	X-RAY DIFFRACTION	121	94
3.751-3.815	0.169	497	X-RAY DIFFRACTION	121	92
3.815-3.885	0.173	556	X-RAY DIFFRACTION	121	92
3.885-3.959	0.166	522	X-RAY DIFFRACTION	121	92
3.959-4.04	0.142	541	X-RAY DIFFRACTION	121	92
4.04-4.128	0.147	548	X-RAY DIFFRACTION	121	92
4.128-4.224	0.146	512	X-RAY DIFFRACTION	121	94
4.224-4.329	0.14	570	X-RAY DIFFRACTION	121	94
4.329-4.446	0.137	517	X-RAY DIFFRACTION	121	94
4.446-4.577	0.138	571	X-RAY DIFFRACTION	121	93
4.577-4.724	0.132	523	X-RAY DIFFRACTION	121	93
4.724-4.893	0.132	543	X-RAY DIFFRACTION	121	94
4.893-5.089	0.137	549	X-RAY DIFFRACTION	121	95
5.089-5.32	0.152	547	X-RAY DIFFRACTION	121	94
5.32-5.6	0.153	542	X-RAY DIFFRACTION	121	93
5.6-5.949	0.173	539	X-RAY DIFFRACTION	121	92
5.949-6.407	0.174	529	X-RAY DIFFRACTION	121	91
6.407-7.049	0.16	548	X-RAY DIFFRACTION	121	94
7.049-8.062	0.169	532	X-RAY DIFFRACTION	121	91
8.062-10.133	0.145	536	X-RAY DIFFRACTION	121	92
10.133-41.138	0.173	546	X-RAY DIFFRACTION	121	91

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