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- PDB-2pr3: Factor XA inhibitor -

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Basic information

Entry
Database: PDB / ID: 2pr3
TitleFactor 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-237 / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsZhang, E. / Kohrt, J.T. / Bigge, C.F. / Finzel, B.C.
CitationJournal: Chem.Biol.Drug Des. / Year: 2007
Title: Structure-based drug design of pyrrolidine-1, 2-dicarboxamides as a novel series of orally bioavailable factor Xa inhibitors
Authors: Van Huis, C.A. / Bigge, C.F. / Casimiro-Garcia, A. / Cody, W.L. / Dudley, D.A. / Filipski, K.J. / Heemstra, R.J. / Kohrt, J.T. / Narasimhan, L.S. / Schaum, R.P. / Zhang, E. / Bryant, J.W. / ...Authors: Van Huis, C.A. / Bigge, C.F. / Casimiro-Garcia, A. / Cody, W.L. / Dudley, D.A. / Filipski, K.J. / Heemstra, R.J. / Kohrt, J.T. / Narasimhan, L.S. / Schaum, R.P. / Zhang, E. / Bryant, J.W. / Haarer, S. / Janiczek, N. / Leadley, R.J. / McClanahan, T. / Thomas Peterson, J. / Welch, K.M. / Edmunds, J.J.
History
DepositionMay 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software

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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
B: COAGULATION FACTOR X, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5335
Polymers31,9072
Non-polymers6263
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-42 kcal/mol
Surface area13270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.485, 72.354, 77.880
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 / 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.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-237 / (2R,4R)-N~1~-(4-CHLOROPHENYL)-N~2~-[3-FLUORO-2'-(METHYLSULFONYL)BIPHENYL-4-YL]-4-METHOXYPYRROLIDINE-1,2-DICARBOXAMIDE


Mass: 546.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25ClFN3O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.5418 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
211
ReflectionResolution: 1.5→50 Å / Num. all: 49540 / Num. obs: 49540 / % possible obs: 95.7 % / Rmerge(I) obs: 0.041 / Χ2: 0.9 / Net I/σ(I): 21.62
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 4.83 / Num. unique all: 3760 / Rsym value: 0.264 / Χ2: 0.974 / % possible all: 74

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→50 Å / FOM work R set: 0.823
RfactorNum. reflection
Rfree0.2667 3565
Rwork0.2554 -
all0.2554 44634
obs-44634
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 39 222 2482
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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