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- PDB-3cen: Factor XA in complex with the inhibitor N-(2-(((5-chloro-2-pyridi... -

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Basic information

Entry
Database: PDB / ID: 3cen
TitleFactor XA in complex with the inhibitor N-(2-(((5-chloro-2-pyridinyl) amino)sulfonyl)phenyl)-4-(2-oxo-1(2H)-pyridinyl)benzamide
Components
  • COAGULATION FACTOR X, HEAVY CHAIN
  • COAGULATION FACTOR X, LIGHT CHAIN
KeywordsHYDROLASE / glycoprotein / serine protease / plasma / blood coagulation factor / protein inhibitor complex / calcium-binding / Cleavage on pair of basic residues / EGF-like domain / Gamma-carboxyglutamic acid / Hydroxylation / Polymorphism / Zymogen
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 / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / 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 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-FXA / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsChang, C.-H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Structure-Activity Relationships of Anthranilamide-Based Factor Xa Inhibitors Containing Piperidinone and Pyridinone P4 Moieties
Authors: Corte, J.R. / Fang, T. / Pinto, D.J.P. / Han, W. / Hu, Z. / Jiang, X.-J. / Li, Y.-L. / Gauuan, J.F. / Hadden, M. / Orton, D. / Rendina, A.R. / Luettgen, J.M. / Wong, P.C. / He, K. / Morin, P. ...Authors: Corte, J.R. / Fang, T. / Pinto, D.J.P. / Han, W. / Hu, Z. / Jiang, X.-J. / Li, Y.-L. / Gauuan, J.F. / Hadden, M. / Orton, D. / Rendina, A.R. / Luettgen, J.M. / Wong, P.C. / He, K. / Morin, P. / Chang, C.-H. / Cheney, D.L. / Knabb, R.M. / Wexler, R.R. / Lam, P.Y.S.
History
DepositionFeb 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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)32,5173
Polymers32,0362
Non-polymers4811
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-10.6 kcal/mol
Surface area13430 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 / Stuart factor / Stuart-Prower factor


Mass: 26447.104 Da / Num. of mol.: 1
Fragment: Activated factor Xa heavy chain, UNP residues 235-468
Source method: isolated from a natural source / Details: PROTEOLYTIC CLEAVAGE PRODUCT / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#2: Protein COAGULATION FACTOR X, LIGHT CHAIN / Stuart factor / Stuart-Prower factor


Mass: 5589.234 Da / Num. of mol.: 1 / Fragment: UNP 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-FXA / N-(2-(((5-CHLORO-2-PYRIDINYL)AMINO)SULFONYL)PHENYL)-4-(2-OXO-1(2H)-PYRIDINYL)BENZAMIDE / N-{2-[(5-chloropyridin-2-yl)sulfamoyl]phenyl}-4-(2-oxopyridin-1(2H)-yl)benzamide


Mass: 480.923 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H17ClN4O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsHOH 302-580 CORRESPOND TO AUTHORS ORIGINAL HOH 2-280

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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 FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 27, 2003 / Details: MICROMAX CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 28031 / % possible obs: 64.2 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 42.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.7 / % possible all: 11.3

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000(DENZO)data reduction
HKL-2000(SCALEPACK)data scaling
CNX2000refinement
RefinementResolution: 1.6→24.7 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1147871.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1563 5.9 %RANDOM
Rwork0.249 ---
obs0.251 26669 61.9 %-
all-28003 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.976 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---4.02 Å20 Å2
3---4.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.6→24.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 33 279 2550
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 1.6→1.67 Å / Rfactor Rfree error: 0.077 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.428 31 5 %
Rwork0.372 584 -
all-615 -
obs--11.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4fxa.paramfxa.top

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