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- PDB-2ftd: Crystal structure of Cathepsin K complexed with 7-Methyl-Substitu... -

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Basic information

Entry
Database: PDB / ID: 2ftd
TitleCrystal structure of Cathepsin K complexed with 7-Methyl-Substituted Azepan-3-one compound
ComponentsCathepsin K
KeywordsHYDROLASE / Sulfhydryl Proteinase
Function / homology
Function and homology information


cathepsin K / thyroid hormone generation / proteolysis involved in protein catabolic process / lysosome / immune response / apical plasma membrane / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Peptidase C1A, cathepsin K / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal ...Peptidase C1A, cathepsin K / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-ILI / Cathepsin K
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.55 Å
AuthorsYamashita, D.S. / Baoguang, Z.
CitationJournal: J.Med.Chem. / Year: 2006
Title: Structure activity relationships of 5-, 6-, and 7-methyl-substituted azepan-3-one cathepsin K inhibitors.
Authors: Yamashita, D.S. / Marquis, R.W. / Xie, R. / Nidamarthy, S.D. / Oh, H.J. / Jeong, J.U. / Erhard, K.F. / Ward, K.W. / Roethke, T.J. / Smith, B.R. / Cheng, H.Y. / Geng, X. / Lin, F. / Offen, P. ...Authors: Yamashita, D.S. / Marquis, R.W. / Xie, R. / Nidamarthy, S.D. / Oh, H.J. / Jeong, J.U. / Erhard, K.F. / Ward, K.W. / Roethke, T.J. / Smith, B.R. / Cheng, H.Y. / Geng, X. / Lin, F. / Offen, P.H. / Wang, B. / Nevins, N. / Head, M.S. / Haltiwanger, R.C. / Narducci Sarjeant, A.A. / Liable-Sands, L.M. / Zhao, B. / Smith, W.W. / Janson, C.A. / Gao, E. / Tomaszek, T. / McQueney, M. / James, I.E. / Gress, C.J. / Zembryki, D.L. / Lark, M.W. / Veber, D.F.
History
DepositionJan 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin K
B: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1284
Polymers47,0472
Non-polymers1,0812
Water3,477193
1
A: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0642
Polymers23,5231
Non-polymers5411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0642
Polymers23,5231
Non-polymers5411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.874, 74.874, 339.555
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Cathepsin K /


Mass: 23523.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Strain: Osteoclast / Gene: CTSK / Production host: unidentified baculovirus / Strain (production host): SF9 / References: UniProt: P61277, cathepsin K
#2: Chemical ChemComp-ILI / N-[(1S)-1-({[(3S,4S,7R)-3-HYDROXY-7-METHYL-1-(PYRIDIN-2-YLSULFONYL)-2,3,4,7-TETRAHYDRO-1H-AZEPIN-4-YL]AMINO}CARBONYL)-3-METHYLBUTYL]-1-BENZOFURAN-2-CARBOXAMIDE


Mass: 540.631 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H32N4O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG 400 as precipitant, in 0.1 M Hepes buffer, at pH 7.5 containing 0.2 M CaCl2, temperature 283K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorDetector: CCD / Date: Apr 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.55→100 Å / Num. all: 19480 / Num. obs: 17372 / % possible obs: 89.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rsym value: 0.058 / Net I/σ(I): 19
Reflection shellResolution: 2.55→2.59 Å / Mean I/σ(I) obs: 10.2 / Num. unique all: 631 / Rsym value: 0.094 / % possible all: 65

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.55→25 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2837 1017 RANDOM
Rwork0.2374 --
all-19480 -
obs-17372 -
Refinement stepCycle: LAST / Resolution: 2.55→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 76 193 3567
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2958
X-RAY DIFFRACTIONc_bond_d0.0082

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