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- PDB-2phb: An Orally Efficacious Factor Xa Inhibitor -

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Basic information

Entry
Database: PDB / ID: 2phb
TitleAn Orally Efficacious Factor Xa Inhibitor
Components
  • Coagulation factor X, heavy chain
  • Coagulation factor X, light chain
KeywordsBLOOD CLOTTING / FXA COAGULATION FACTOR INHIBITOR
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 leukocyte chemotaxis / 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 ...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 leukocyte chemotaxis / 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 / Coagulation Factor Xa inhibitory site / Laminin / 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. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Laminin / Coagulation Factor Xa inhibitory site / Laminin / 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 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-230 / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsZhang, E. / Kohrt, J.T. / Bigge, C.F. / Finzel, B.C.
CitationJournal: Chem.Biol.Drug Des. / Year: 2007
Title: The discovery of (2R,4R)-N-(4-chlorophenyl)-N- (2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl)-4-methoxypyrrolidine-1,2-dicarboxamide (PD 0348292), an orally efficacious factor Xa inhibitor
Authors: Kohrt, J.T. / Bigge, C.F. / Bryant, J.W. / Casimiro-Garcia, A. / Chi, L. / Cody, W.L. / Dahring, T. / Dudley, D.A. / Filipski, K.J. / Haarer, S. / Heemstra, R. / Janiczek, N. / Narasimhan, L. ...Authors: Kohrt, J.T. / Bigge, C.F. / Bryant, J.W. / Casimiro-Garcia, A. / Chi, L. / Cody, W.L. / Dahring, T. / Dudley, D.A. / Filipski, K.J. / Haarer, S. / Heemstra, R. / Janiczek, N. / Narasimhan, L. / McClanahan, T. / Peterson, J.T. / Sahasrabudhe, V. / Schaum, R. / Van Huis, C.A. / Welch, K.M. / Zhang, E. / Leadley, R.J. / Edmunds, J.J.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,4324
Polymers31,9072
Non-polymers5252
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-19.8 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.483, 72.406, 77.715
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 X, heavy chain / E.C.3.4.21.6 / Stuart factor / heavy chain / Stuart- Prower factor / heavy chain / Activated factor Xa heavy chain


Mass: 26447.104 Da / Num. of mol.: 1 / Fragment: heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F10 / Production host: Escherichia coli (E. coli) / References: UniProt: P00742, coagulation factor Xa
#2: Protein Coagulation factor X, light chain / E.C.3.4.21.6 / Stuart factor / light chain / Stuart- Prower factor / light chain / Activated factor Xa light chain


Mass: 5460.055 Da / Num. of mol.: 1 / Fragment: light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F10 / Production host: Escherichia coli (E. coli) / References: UniProt: P00742, coagulation factor Xa
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-230 / (2R,4R)-N~1~-(4-CHLOROPHENYL)-N~2~-[2-FLUORO-4-(2-OXOPYRIDIN-1(2H)-YL)PHENYL]-4-METHOXYPYRROLIDINE-1,2-DICARBOXAMIDE / PD-0348292


Mass: 484.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22ClFN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 50.59 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→41.604 Å / Num. obs: 15260 / % possible obs: 90.8 % / Rmerge(I) obs: 0.111 / Χ2: 0.992 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.280.41816350.73599.7
2.28-2.370.34416320.75199.4
2.37-2.480.26816390.80599
2.48-2.610.23416200.85598.3
2.61-2.770.18516170.93296.9
2.77-2.990.14315961.01195.2
2.99-3.290.10315201.14391.6
3.29-3.760.07914431.36185.1
3.76-4.740.06512021.43570.3
4.74-500.05313561.48774.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.296 -random
Rwork0.26 --
all0.26 11511 -
obs-11511 -
Displacement parametersBiso mean: 41.604 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 35 50 2314

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