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- PDB-3ffg: Factor XA in complex with the inhibitor (R)-6-(2'-((3- HYDROXYPYR... -

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Basic information

Entry
Database: PDB / ID: 3ffg
TitleFactor XA in complex with the inhibitor (R)-6-(2'-((3- HYDROXYPYRROLIDIN-1-YL)METHYL)BIPHENYL-4-YL)-1-(3-(5-OXO-4,5-DIHYDRO-1H-1,2,4-TRIAZOL-3-YL)PHENYL)-3-(TRIFLUOROMETHYL)-5,6-DIHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN- 7(4H)-ONE
Components
  • Coagulation factor X, heavy chainFactor X
  • Coagulation factor X, light chainFactor X
KeywordsHYDROLASE / GLYCOPROTEIN / SERINE PROTEASE / PLASMA / BLOOD COAGULATION FACTOR / PROTEIN INHIBITOR COMPLEX / CALCIUM- BINDING / Blood coagulation / Calcium / Cleavage on pair of basic residues / Protease / Secreted
Function / homology
Function and homology information


coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / 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-FFG / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.54 Å
AuthorsAlexander, R.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: Phenyltriazolinones as potent factor Xa inhibitors.
Authors: Quan, M.L. / Pinto, D.J. / Rossi, K.A. / Sheriff, S. / Alexander, R.S. / Amparo, E. / Kish, K. / Knabb, R.M. / Luettgen, J.M. / Morin, P. / Smallwood, A. / Woerner, F.J. / Wexler, R.R.
History
DepositionDec 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor X, heavy chain
L: Coagulation factor X, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6523
Polymers32,0362
Non-polymers6161
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-10 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.900, 72.500, 78.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coagulation factor X, heavy chain / Factor X / factor Xa heavy chain / Stuart factor / Stuart-Prower factor / Factor X heavy chain


Mass: 26447.104 Da / Num. of mol.: 1 / Fragment: sequence database residues 235-468 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#2: Protein Coagulation factor X, light chain / Factor X / factor X light chain / Stuart factor / Stuart-Prower factor


Mass: 5589.234 Da / Num. of mol.: 1 / Fragment: sequence database residues 127-178 / Source method: isolated from a natural source / Details: Proteolytic cleavage product / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#3: Chemical ChemComp-FFG / (R)-6-(2'-((3-hydroxypyrrolidin-1-yl)methyl)biphenyl-4-yl)-1-(3-(5-oxo-4,5-dihydro-1h-1,2,4-triazol-3-yl)phenyl)-3-(trifluoromethyl)-5,6-dihydro-1h-pyrazolo[3,4-c]pyridin-7(4h)-one / 6-(2'-{[(3R)-3-hydroxypyrrolidin-1-yl]methyl}biphenyl-4-yl)-1-[3-(5-oxo-4,5-dihydro-1H-1,2,4-triazol-3-yl)phenyl]-3-(trifluoromethyl)-1,4,5,6-tetrahydro-7H-pyrazolo[3,4-c]pyridin-7-one


Mass: 615.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H28F3N7O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 200 mM Sodium Acetate, pH 5.5, 18% PEG6000, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 9, 2001 / Details: BLUE CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 49553 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.3 Å2
Reflection shellHighest resolution: 1.54 Å

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000(DENZO)data reduction
HKL-2000(SCALEPACK)data scaling
CNX2005refinement
RefinementResolution: 1.54→19.46 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0 / Data cutoff high absF: 782288 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2795 6 %RANDOM
Rwork0.215 ---
obs0.216 46641 95.4 %-
all-46687 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.339 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso max: 74.7 Å2 / Biso mean: 21.66 Å2 / Biso min: 8.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2---2.74 Å20 Å2
3---4.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.54→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 45 253 2541
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.58
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 1.54→1.61 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.333 337 6.1 %
Rwork0.299 5150 -
all-5487 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMLIGAND.TOP
X-RAY DIFFRACTION5LIGAND.PAR

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