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

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Basic information

Entry
Database: PDB / ID: 2zeb
TitlePotent, Nonpeptide Inhibitors of Human Mast Cell Tryptase
ComponentsTryptase beta 2
KeywordsHYDROLASE / 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
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-11M / Tryptase alpha/beta-1 / Tryptase alpha/beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsSpurlino, J.C. / Lewandowski, F. / Milligan, C.
CitationJournal: 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. / ...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. / Abraham, W.M. / Boswell-Smith, V. / Page, C.P. / Maryanoff, B.E.
History
DepositionDec 8, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptase beta 2
B: Tryptase beta 2
C: Tryptase beta 2
D: Tryptase beta 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7598
Polymers109,0614
Non-polymers1,6984
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-42 kcal/mol
Surface area38450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.670, 82.670, 171.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#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-11M / 1-(1'-{[3-(methylsulfanyl)-2-benzothiophen-1-yl]carbonyl}spiro[1-benzofuran-3,4'-piperidin]-5-yl)methanamine


Mass: 424.579 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H24N2O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.24 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 38453 / Biso Wilson estimate: 28.627 Å2

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.5→30 Å / FOM work R set: 0.844 / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.225 1945 5.06 %
Rwork0.172 --
obs-38453 96.48 %
Solvent computationBsol: 22.923 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 96.32 Å2 / Biso mean: 29.31 Å2 / Biso min: 12.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.949 Å2-0 Å20 Å2
2---1.949 Å2-0 Å2
3---3.898 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7648 0 116 299 8063
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.7671
X-RAY DIFFRACTIONf_bond_d0.0061
X-RAY DIFFRACTIONf_chiral_restr0.0591
X-RAY DIFFRACTIONf_dihedral_angle_d13.1361
X-RAY DIFFRACTIONf_plane_restr0.0041
X-RAY DIFFRACTIONf_nbd_refined4.0861
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.497-2.5080.183311X-RAY DIFFRACTION7358
2.508-2.520.191488X-RAY DIFFRACTION7390
2.52-2.5320.19483X-RAY DIFFRACTION7389
2.532-2.5440.195470X-RAY DIFFRACTION7387
2.544-2.5560.18469X-RAY DIFFRACTION7387
2.556-2.5690.211508X-RAY DIFFRACTION7391
2.569-2.5820.192491X-RAY DIFFRACTION7391
2.582-2.5950.194499X-RAY DIFFRACTION7390
2.595-2.6090.192467X-RAY DIFFRACTION7391
2.609-2.6220.194472X-RAY DIFFRACTION7389
2.622-2.6360.195488X-RAY DIFFRACTION7388
2.636-2.6510.197501X-RAY DIFFRACTION7387
2.651-2.6650.199479X-RAY DIFFRACTION7387
2.665-2.680.2482X-RAY DIFFRACTION7393
2.68-2.6960.193464X-RAY DIFFRACTION7388
2.696-2.7110.195494X-RAY DIFFRACTION7391
2.711-2.7270.215489X-RAY DIFFRACTION7389
2.727-2.7440.2505X-RAY DIFFRACTION7390
2.744-2.7610.205514X-RAY DIFFRACTION7391
2.761-2.7780.198463X-RAY DIFFRACTION7391
2.778-2.7960.207486X-RAY DIFFRACTION7390
2.796-2.8140.211499X-RAY DIFFRACTION7392
2.814-2.8320.201523X-RAY DIFFRACTION7391
2.832-2.8510.199485X-RAY DIFFRACTION7391
2.851-2.8710.215523X-RAY DIFFRACTION7392
2.871-2.8910.2480X-RAY DIFFRACTION7392
2.891-2.9120.226498X-RAY DIFFRACTION7392
2.912-2.9340.197514X-RAY DIFFRACTION7391
2.934-2.9550.203481X-RAY DIFFRACTION7391
2.955-2.9780.207496X-RAY DIFFRACTION7391
2.978-3.0020.21498X-RAY DIFFRACTION7393
3.002-3.0260.204495X-RAY DIFFRACTION7392
3.026-3.0510.214518X-RAY DIFFRACTION7392
3.051-3.0770.197528X-RAY DIFFRACTION7393
3.077-3.1030.2465X-RAY DIFFRACTION7393
3.103-3.1310.203506X-RAY DIFFRACTION7392
3.131-3.160.195518X-RAY DIFFRACTION7392
3.16-3.190.199514X-RAY DIFFRACTION7392
3.19-3.2210.19487X-RAY DIFFRACTION7393
3.221-3.2530.178493X-RAY DIFFRACTION7393
3.253-3.2860.192520X-RAY DIFFRACTION7393
3.286-3.3210.18513X-RAY DIFFRACTION7394
3.321-3.3580.182519X-RAY DIFFRACTION7394
3.358-3.3960.161510X-RAY DIFFRACTION7394
3.396-3.4360.169508X-RAY DIFFRACTION7392
3.436-3.4780.16503X-RAY DIFFRACTION7393
3.478-3.5220.166494X-RAY DIFFRACTION7394
3.522-3.5680.162519X-RAY DIFFRACTION7393
3.568-3.6170.166504X-RAY DIFFRACTION7394
3.617-3.6690.15521X-RAY DIFFRACTION7393
3.669-3.7230.151507X-RAY DIFFRACTION7392
3.723-3.7810.153515X-RAY DIFFRACTION7394
3.781-3.8430.166485X-RAY DIFFRACTION7393
3.843-3.910.144524X-RAY DIFFRACTION7394
3.91-3.9810.141495X-RAY DIFFRACTION7393
3.981-4.0570.133527X-RAY DIFFRACTION7393
4.057-4.140.129514X-RAY DIFFRACTION7393
4.14-4.230.133498X-RAY DIFFRACTION7394
4.23-4.3280.13537X-RAY DIFFRACTION7393
4.328-4.4360.12498X-RAY DIFFRACTION7394
4.436-4.5560.124503X-RAY DIFFRACTION7395
4.556-4.690.13531X-RAY DIFFRACTION7394
4.69-4.8410.122530X-RAY DIFFRACTION7394
4.841-5.0140.135503X-RAY DIFFRACTION7395
5.014-5.2140.133510X-RAY DIFFRACTION7393
5.214-5.4510.147520X-RAY DIFFRACTION7394
5.451-5.7380.148521X-RAY DIFFRACTION7394
5.738-6.0960.167513X-RAY DIFFRACTION7395
6.096-6.5650.157524X-RAY DIFFRACTION7395
6.565-7.2220.167523X-RAY DIFFRACTION7395
7.222-8.260.163537X-RAY DIFFRACTION7394
8.26-10.3780.141518X-RAY DIFFRACTION7394
10.378-40.8850.172520X-RAY DIFFRACTION7393

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