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- PDB-2bz6: Orally available Factor7a inhibitor -

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Basic information

Entry
Database: PDB / ID: 2bz6
TitleOrally available Factor7a inhibitor
Components(BLOOD COAGULATION FACTOR ...) x 2
KeywordsHYDROLASE / SERINE PROTEASE / COAGULATION / ENZYME COMPLEX
Function / homology
Function and homology information


coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to carbon dioxide / serine-type peptidase complex / response to genistein / response to vitamin K / positive regulation of platelet-derived growth factor receptor signaling pathway ...coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to carbon dioxide / serine-type peptidase complex / response to genistein / response to vitamin K / positive regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of leukocyte chemotaxis / response to thyroxine / response to cholesterol / positive regulation of positive chemotaxis / response to growth hormone / : / positive regulation of blood coagulation / animal organ regeneration / positive regulation of TOR signaling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / BMAL1:CLOCK,NPAS2 activates circadian expression / serine-type peptidase activity / circadian rhythm / protein processing / response to estrogen / Golgi lumen / blood coagulation / response to estradiol / extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / : / 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 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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-346 / Coagulation factor VII
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.6 Å
AuthorsGroebke-Zbinden, K. / Obst-Sander, U. / Hilpert, K. / Kuehne, H. / Banner, D.W. / Boehm, H.J. / Stahl, M. / Ackermann, J. / Alig, L. / Weber, L. ...Groebke-Zbinden, K. / Obst-Sander, U. / Hilpert, K. / Kuehne, H. / Banner, D.W. / Boehm, H.J. / Stahl, M. / Ackermann, J. / Alig, L. / Weber, L. / Wessel, H.P. / Riederer, M.A. / Tschopp, T.B. / Lave, T.
CitationJournal: Bioorg.Med.Chem. / Year: 2006
Title: Dose-Dependant Antithrombotic Activity of an Orally Active Tissue Factor/Factor Viia Inhibitor without Concomitant Enhancement of Bleeding Propensity.
Authors: Groebke-Zbinden, K. / Banner, D.W. / Hilpert, K. / Himber, J. / Lave, T. / Riederer, M.A. / Stahl, M. / Tschopp, T.B. / Obst-Sander, U.
History
DepositionAug 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: BLOOD COAGULATION FACTOR VIIA
L: BLOOD COAGULATION FACTOR VIIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4015
Polymers33,8482
Non-polymers5543
Water9,008500
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-10.9 kcal/mol
Surface area16580 Å2
MethodPQS
Unit cell
Length a, b, c (Å)94.930, 94.930, 115.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11H-2100-

HOH

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Components

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BLOOD COAGULATION FACTOR ... , 2 types, 2 molecules HL

#1: Protein BLOOD COAGULATION FACTOR VIIA / SERUM PROTHROMBIN CONVERSION ACCELERATOR / SPCA / PROCONVERTIN / EPTACOG ALFA / NOVOSEVEN


Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: FACTOR VII HEAVY CHAIN, RESIDUES 213-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P08709, coagulation factor VIIa
#2: Protein BLOOD COAGULATION FACTOR VIIA / SERUM PROTHROMBIN CONVERSION ACCELERATOR / SPCA / PROCONVERTIN / EPTACOG ALFA / NOVOSEVEN


Mass: 5744.453 Da / Num. of mol.: 1 / Fragment: FACTOR VII LIGHT CHAIN, RESIDUES 150-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P08709, coagulation factor VIIa

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Non-polymers , 4 types, 503 molecules

#3: Chemical ChemComp-346 / (R)-(4-CARBAMIMIDOYL-PHENYLAMINO)-[5-ETHOXY-2-FLUORO-3-[(R)-TETRAHYDRO-FURAN-3-YLOXY]-PHENYL]-ACETIC ACID / (2R)-({4-[AMINO(IMINO)METHYL]PHENYL}AMINO){5-ETHOXY-2-FLUORO-3-[(3R)-TETRAHYDROFURAN-3-YLOXY]PHENYL}ACETIC ACID


Mass: 417.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24FN3O5
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.12 Å3/Da / Density % sol: 60.2 % / Description: ISOMORPHOUS TO 1W7X.PDB
Crystal growpH: 8.5
Details: 35%AS, 2%PEG400, 100MM BICINE PH8.5, 15% GLYCEROL, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8
DetectorType: MARRESEARCH MAR300 / Detector: IMAGE PLATE / Date: Feb 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 69242 / % possible obs: 81.6 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.15
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.78 / % possible all: 36.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.6→73.32 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.579 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3045 5 %RANDOM
Rwork0.166 ---
obs0.168 58180 90.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2---0.51 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→73.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 36 500 2906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212562
X-RAY DIFFRACTIONr_bond_other_d0.0010.022284
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.973508
X-RAY DIFFRACTIONr_angle_other_deg0.80935313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69223.178107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05115407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7931519
X-RAY DIFFRACTIONr_chiral_restr0.0830.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02526
X-RAY DIFFRACTIONr_nbd_refined0.2180.2464
X-RAY DIFFRACTIONr_nbd_other0.1930.22421
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21205
X-RAY DIFFRACTIONr_nbtor_other0.0810.21567
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2351
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0760.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9041.52035
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06222572
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6631152
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2664.5936
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.274 253
Rwork0.253 4720
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6275-0.1156-0.39250.81050.15470.62930.04540.14040.3046-0.0432-0.0125-0.0703-0.03750.0693-0.0329-0.05570.01180.00820.03390.0079-0.037541.32827.28242.381
20.935-0.05450.21561.0137-0.09990.8568-0.00290.11560.0352-0.0509-0.00370.0209-0.08510.02830.0066-0.041-0.0002-0.0070.007-0.0042-0.080819.61734.65438.218
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L90 - 142
2X-RAY DIFFRACTION2H16 - 257

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