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- PDB-2g00: Factor Xa in complex with the inhibitor 3-(6-(2'-((dimethylamino)... -

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Basic information

Entry
Database: PDB / ID: 2g00
TitleFactor Xa in complex with the inhibitor 3-(6-(2'-((dimethylamino)methyl)-4-biphenylyl)-7-oxo-3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-c]pyridin-1-yl)benzamide
Components(Coagulation factor X) x 2
KeywordsHYDROLASE / GLYCOPROTEIN / SERINE PROTEASE / PLASMA / BLOOD COAGULATION FACTOR / PROTEIN INHIBITOR COMPLEX / CALCIUM-BINDING
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-4QC / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.1 Å
AuthorsAlexander, R.S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Discovery of potent, efficacious, and orally bioavailable inhibitors of blood coagulation factor Xa with neutral P1 moieties.
Authors: Pinto, D.J. / Galemmo, R.A. / Quan, M.L. / Orwat, M.J. / Clark, C. / Li, R. / Wells, B. / Woerner, F. / Alexander, R.S. / Rossi, K.A. / Smallwood, A. / Wong, P.C. / Luettgen, J.M. / Rendina, ...Authors: Pinto, D.J. / Galemmo, R.A. / Quan, M.L. / Orwat, M.J. / Clark, C. / Li, R. / Wells, B. / Woerner, F. / Alexander, R.S. / Rossi, K.A. / Smallwood, A. / Wong, P.C. / Luettgen, J.M. / Rendina, A.R. / Knabb, R.M. / He, K. / Wexler, R.R. / Lam, P.Y.
History
DepositionFeb 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
L: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5703
Polymers32,0362
Non-polymers5341
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-2 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.600, 72.400, 78.900
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: Coagulation Factor X, Heavy Chain / 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 / Stuart factor / Stuart-Prower factor


Mass: 5589.234 Da / Num. of mol.: 1 / Fragment: Coagulation Factor X, Light Chain / 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-4QC / 3-[6-{2'-[(DIMETHYLAMINO)METHYL]BIPHENYL-4-YL}-7-OXO-3-(TRIFLUOROMETHYL)-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN-1-YL]BENZAMIDE


Mass: 533.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H26F3N5O2
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.24 %

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→19.92 Å / Num. obs: 18375 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.085 / Χ2: 1.507 / Net I/σ(I): 4.8
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2% possible all
2.1-2.1498.33.90.3482.59150.36298.3
2.14-2.1795.10.3268890.339
2.17-2.2198.70.2649050.328
2.21-2.2695.80.2329210.345
2.26-2.3198.90.2199080.319
2.31-2.3696.40.1859060.365
2.36-2.4298.80.1879390.444
2.42-2.48970.1699040.634
2.48-2.5598.80.1649340.593
2.55-2.6398.40.1419290.535
2.63-2.7297.50.1279110.457
2.72-2.82980.1169300.943
2.82-2.9598.60.1159321.109
2.95-3.0997.60.1069161.353
3.09-3.2897.40.0849481.236
3.28-3.5196.40.0679042.009
3.51-3.8395.40.0659313.223
3.83-4.3950.0579195.414
4.3-5.1793.20.0489214.082
5.17-890.10.0589135.602

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000(DENZO)data reduction
HKL-2000(SCALEPACK)data scaling
EPMRphasing
CNX2000.1refinement
RefinementMethod to determine structure: molecular replacement / Resolution: 2.1→19.92 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 481577.719 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1068 5.9 %RANDOM
Rwork0.269 ---
all0.27 18672 --
obs-18188 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.93 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2---4.25 Å20 Å2
3---3.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 39 0 2277
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.35 129 6.3 %
Rwork0.356 1925 -
obs-2054 85.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION54QC.par4QC.top

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