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- PDB-6ts7: Coagulation factor XI protease domain in complex with active site... -

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Basic information

Entry
Database: PDB / ID: 6ts7
TitleCoagulation factor XI protease domain in complex with active site inhibitor
ComponentsCoagulation factor XI
KeywordsHYDROLASE / S1 protease / serine protease / structure-based drug design / active site directed inhibitor
Function / homology
Function and homology information


coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 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. ...Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 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 family, serine active site. / Serine proteases, trypsin domain profile. / 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-NWE / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.63 Å
AuthorsRenatus, M. / Schiering, N.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structure-Based Design and Preclinical Characterization of Selective and Orally Bioavailable Factor XIa Inhibitors: Demonstrating the Power of an Integrated S1 Protease Family Approach.
Authors: Lorthiois, E. / Roache, J. / Barnes-Seeman, D. / Altmann, E. / Hassiepen, U. / Turner, G. / Duvadie, R. / Hornak, V. / Karki, R.G. / Schiering, N. / Weihofen, W.A. / Perruccio, F. / Calhoun, ...Authors: Lorthiois, E. / Roache, J. / Barnes-Seeman, D. / Altmann, E. / Hassiepen, U. / Turner, G. / Duvadie, R. / Hornak, V. / Karki, R.G. / Schiering, N. / Weihofen, W.A. / Perruccio, F. / Calhoun, A. / Fazal, T. / Dedic, D. / Durand, C. / Dussauge, S. / Fettis, K. / Tritsch, F. / Dentel, C. / Druet, A. / Liu, D. / Kirman, L. / Lachal, J. / Namoto, K. / Bevan, D. / Mo, R. / Monnet, G. / Muller, L. / Zessis, R. / Huang, X. / Lindsley, L. / Currie, T. / Chiu, Y.H. / Fridrich, C. / Delgado, P. / Wang, S. / Hollis-Symynkywicz, M. / Berghausen, J. / Williams, E. / Liu, H. / Liang, G. / Kim, H. / Hoffmann, P. / Hein, A. / Ramage, P. / D'Arcy, A. / Harlfinger, S. / Renatus, M. / Ruedisser, S. / Feldman, D. / Elliott, J. / Sedrani, R. / Maibaum, J. / Adams, C.M.
History
DepositionDec 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coagulation factor XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2302
Polymers26,8561
Non-polymers3731
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.690, 60.490, 64.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coagulation factor XI / FXI / Plasma thromboplastin antecedent / PTA


Mass: 26856.496 Da / Num. of mol.: 1 / Mutation: SER A 123 SWS P03951 CYS 500 ENGINEERED MUTATION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Escherichia coli (E. coli) / References: UniProt: P03951, coagulation factor XIa
#2: Chemical ChemComp-NWE / 2-[2-[[3-(1,2,3,4-tetrahydroisoquinolin-7-yl)phenyl]methoxy]phenyl]ethanoic acid


Mass: 373.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 25% w/v PEG 3350, Sodium acetate trihydrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99995 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 2.63→63.99 Å / Num. obs: 7265 / % possible obs: 99.8 % / Redundancy: 5.998 % / Biso Wilson estimate: 34.976 Å2 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.17 / Χ2: 0.938 / Net I/σ(I): 10.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
2.63-2.76.0520.5273.725160.57899.6
2.7-2.775.8780.4644.275180.5199.8
2.77-2.855.6650.4024.685020.445100
2.85-2.945.790.365.534820.398100
2.94-3.046.1880.2787.174830.30499.2
3.04-3.146.3070.2558.044530.279100
3.14-3.266.3180.2129.794340.231100
3.26-3.46.2650.17610.834230.19299.5
3.4-3.556.0890.16711.594180.183100
3.55-3.725.7550.15512.083870.171100
3.72-3.925.8960.14112.883660.15599.7
3.92-4.166.370.12214.763540.134100
4.16-4.456.2570.11215.783420.122100
4.45-4.86.1470.10616.413130.116100
4.8-5.265.7190.10515.492950.11699.7
5.26-5.885.7210.11414.82690.12599.6
5.88-6.796.160.1115.512380.1299.2
6.79-8.325.8780.09915.522050.109100
8.32-11.765.2380.07816.911640.08799.4
11.76-63.995.1550.08318.051030.093100

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Processing

Software
NameVersionClassification
XSCALEJanuary 30, 2009data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.63→44 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.829 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.389
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 365 -RANDOM
Rwork0.1895 ---
obs0.1938 7264 99.8 %-
Displacement parametersBiso mean: 30.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.7002 Å20 Å20 Å2
2--4.9243 Å20 Å2
3----5.6245 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.63→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 28 97 2000
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081955HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.032652HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d672SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes326HARMONIC5
X-RAY DIFFRACTIONt_it1955HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion249SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1592SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion19.32
LS refinement shellResolution: 2.63→2.94 Å
RfactorNum. reflection% reflection
Rfree0.3432 26 -
Rwork0.2812 --
obs--100 %

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