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- PDB-3m36: Factor XA in complex with the inhibitor 1-[3-(aminomethyl)phenyl]... -

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Basic information

Entry
Database: PDB / ID: 3m36
TitleFactor XA in complex with the inhibitor 1-[3-(aminomethyl)phenyl]-N-[3-fluoro-2'-(methylsulfonyl)biphenyl-4-yl]-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide (DPC423)
Components(Coagulation factor X) x 2
KeywordsHYDROLASE / GLYCOPROTEIN / SERINE PROTEASE / PLASMA / BLOOD COAGULATION FACTOR / PROTEIN INHIBITOR COMPLEX / CALCIUM- BINDING / Blood coagulation / Cleavage on pair of basic residues / Disulfide bond / EGF-like domain / Gamma-carboxyglutamic acid / Polymorphism / Protease / Secreted / 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-M35 / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsAlexander, R.S.
CitationJournal: J.Med.Chem. / Year: 2003
Title: Discovery of 1-(2-Aminomethylphenyl)-3-trifluoromethyl-N-[3-fluoro-2'-(aminosulfonyl)[1,1'-biphenyl)]-1H-pyrazole-5-carboxyamide (DPC602), a Potent, Selective, and Orally Bioavailable Factor Xa Inhibitor
Authors: Pruitt, J.R. / Pinto, D.J.P. / Galemmo, R.A.Jr. / Alexander, R.S. / Rossi, K.A. / Wells, B.L. / Drummond, S. / Bostrom, L.L. / Burdick, D. / Bruckner, R. / Chen, H. / Smallwood, A. / Wong, P. ...Authors: Pruitt, J.R. / Pinto, D.J.P. / Galemmo, R.A.Jr. / Alexander, R.S. / Rossi, K.A. / Wells, B.L. / Drummond, S. / Bostrom, L.L. / Burdick, D. / Bruckner, R. / Chen, H. / Smallwood, A. / Wong, P.C. / Wright, M.R. / Bai, S. / Luettgen, J.M. / Knabb, R.M. / Lam, P.Y.S. / Wexler, R.R.
History
DepositionMar 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: 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: Coagulation factor X
L: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6094
Polymers32,0362
Non-polymers5732
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-23 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.800, 72.300, 77.700
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 / Stuart factor / Stuart-Prower factor


Mass: 26447.104 Da / Num. of mol.: 1 / Fragment: Peptidase S1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#2: Protein Coagulation factor X / 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 / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#3: Chemical ChemComp-M35 / 1-[3-(aminomethyl)phenyl]-N-[3-fluoro-2'-(methylsulfonyl)biphenyl-4-yl]-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide


Mass: 532.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H20F4N4O3S
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
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: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 6, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→19.74 Å / Num. obs: 24383 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.8 Å2
Reflection shellHighest resolution: 1.89 Å

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000(DENZO)data reduction
HKL-2000(SCALEPACK)data scaling
EPMRphasing
CNX2005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→19.74 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 0 / Data cutoff high absF: 62879 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1047 6.1 %RANDOM
Rwork0.223 ---
obs0.226 17205 95.8 %-
all-17214 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.46 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso max: 66.86 Å2 / Biso mean: 29.8 Å2 / Biso min: 11.48 Å2
Baniso -1Baniso -2Baniso -3
1--6.62 Å20 Å20 Å2
2---7.39 Å20 Å2
3---14.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.15→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 38 153 2429
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_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2.15→2.25 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.337 119 5.7 %
Rwork0.29 1974 -
all-2093 -
obs--95.5 %
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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