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- PDB-1v3x: Factor Xa in complex with the inhibitor 1-[6-methyl-4,5,6,7-tetra... -

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Basic information

Entry
Database: PDB / ID: 1v3x
TitleFactor Xa in complex with the inhibitor 1-[6-methyl-4,5,6,7-tetrahydrothiazolo(5,4-c)pyridin-2-yl] carbonyl-2-carbamoyl-4-(6-chloronaphth-2-ylsulphonyl)piperazine
Components
  • Coagulation factor X, HEAVY CHAIN
  • Coagulation factor X, LIGHT CHAIN
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 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-D76 / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / RIGID BODY REFINEMENT / Resolution: 2.2 Å
AuthorsSuzuki, M.
Citation
Journal: J.Med.Chem. / Year: 2004
Title: Synthesis and conformational analysis of a non-amidine factor Xa inhibitor that incorporates 5-methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridine as S4 binding element
Authors: Haginoya, N. / Kobayashi, S. / Komoriya, S. / Yoshino, T. / Suzuki, M. / Shimada, T. / Watanabe, K. / Hirokawa, Y. / Furugori, T. / Nagahara, T.
#1: Journal: Proc.Natl.Acad.Sci.Usa / Year: 1998
Title: Structural basis for chemical inhibition of human blood coagulation factor Xa
Authors: Kamata, K. / Kawamoto, H. / Honma, T. / Iwama, T. / Kim, S.H.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: X-ray structure of active site-inhibited clotting factor Xa. Implications for drug design and substrate recognition
Authors: Brandstetter, H. / Kuhne, A. / Bode, W. / Huber, R. / von der Saal, W. / Wirthensohn, K. / Engh, R.A.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Structure of human des(1-45) factor Xa at 2.2 A resolution
Authors: Padmanabhan, K. / Padmanabhan, K.P. / Tulinsky, A. / Park, C.H. / Bode, W. / Huber, R. / Blankenship, D.T. / Cardin, A.D. / Kisiel, W.
History
DepositionNov 7, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: Coagulation factor X, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5495
Polymers31,9352
Non-polymers6143
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-51 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.050, 71.927, 78.799
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 / Factor Xa heavy chain / Activated factor Xa heavy chain


Mass: 26346.000 Da / Num. of mol.: 1 / Fragment: Residues 16-243 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#2: Protein Coagulation factor X, LIGHT CHAIN / Factor Xa light chain


Mass: 5589.234 Da / Num. of mol.: 1 / Fragment: Residues 87-138 / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-D76 / (2R)-4-[(6-CHLORO-2-NAPHTHYL)SULFONYL]-1-[(5-METHYL-4,5,6,7-TETRAHYDRO[1,3]THIAZOLO[5,4-C]PYRIDIN-2-YL)CARBONYL]PIPERAZ INE-2-CARBOXAMIDE / 1-[6-METHYL-4,5,6,7-TETRAHYDROTHIAZOLO(5,4-C)PYRIDIN-2-YL] CARBONYL-2-CARBAMOYL-4-(6-CHLORONAPHTH-2-YLSULPHONYL)PIPERAZINE


Mass: 534.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24ClN5O4S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 50.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, macro-seeding, soaking / pH: 5
Details: PEG6000, sodium acetate, Malate imidazole, Calcium chloride, pH 5.00, vapor diffusion, macro-seeding, Soaking, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 3, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.5421
21.54181
ReflectionResolution: 2.2→53.124 Å / Num. all: 15999 / Num. obs: 15999 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 35.621 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 13.6
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1332 / Rsym value: 0.259 / % possible all: 90.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: 1FAX

1fax


Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.151 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23302 751 4.7 %RANDOM
Rwork0.1917 ---
all0.19374 15207 --
obs0.19374 15207 100 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CALCULATION
Displacement parametersBiso mean: 35.912 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å20 Å2
2---2.16 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 37 161 2344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212235
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.9643036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9715283
X-RAY DIFFRACTIONr_chiral_restr0.1170.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021685
X-RAY DIFFRACTIONr_nbd_refined0.2140.21026
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2196
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.219
X-RAY DIFFRACTIONr_mcbond_it1.5821.51406
X-RAY DIFFRACTIONr_mcangle_it2.6042.52243
X-RAY DIFFRACTIONr_scbond_it2.3392829
X-RAY DIFFRACTIONr_scangle_it3.3313793
LS refinement shellResolution: 2.2→2.277 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.258 65
Rwork0.176 1370

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