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- PDB-4ng9: Factor viia in complex with the inhibitor (2R)-2-[(1-aminoisoquin... -

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Basic information

Entry
Database: PDB / ID: 4ng9
TitleFactor viia in complex with the inhibitor (2R)-2-[(1-aminoisoquinolin-6-yl)amino]-2-[3-ethoxy-4-(propan-2-yloxy)phenyl]-n-(3-sulfamoylbenzyl)ethanamide
Components
  • Factor VIIa (Heavy Chain)
  • Factor VIIa (Light Chain)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / GLYCOPROTEIN / HYDROLASE / SERINE PROTEASE / PLASMA / BLOOD COAGULATION FACTOR / PROTEIN INHIBITOR COMPLEX / CALCIUM-BINDING / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide ...coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide / response to thyroxine / positive regulation of leukocyte chemotaxis / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / protein processing / Golgi lumen / circadian rhythm / response to estrogen / blood coagulation / response to estradiol / collagen-containing extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / 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 / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / 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-2KE / Coagulation factor VII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWei, A. / Anumula, R.
CitationJournal: ACS Med Chem Lett / Year: 2014
Title: Design and Synthesis of Phenylpyrrolidine Phenylglycinamides As Highly Potent and Selective TF-FVIIa Inhibitors.
Authors: Zhang, X. / Jiang, W. / Jacutin-Porte, S. / Glunz, P.W. / Zou, Y. / Cheng, X. / Nirschl, A.H. / Wurtz, N.R. / Luettgen, J.M. / Rendina, A.R. / Luo, G. / Harper, T.M. / Wei, A. / Anumula, R. ...Authors: Zhang, X. / Jiang, W. / Jacutin-Porte, S. / Glunz, P.W. / Zou, Y. / Cheng, X. / Nirschl, A.H. / Wurtz, N.R. / Luettgen, J.M. / Rendina, A.R. / Luo, G. / Harper, T.M. / Wei, A. / Anumula, R. / Cheney, D.L. / Knabb, R.M. / Wong, P.C. / Wexler, R.R. / Priestley, E.S.
History
DepositionNov 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.formula_weight
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_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
H: Factor VIIa (Heavy Chain)
L: Factor VIIa (Light Chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,31010
Polymers34,1342
Non-polymers1,1768
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-6 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.170, 95.170, 117.490
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-582-

HOH

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Components

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Protein , 2 types, 2 molecules HL

#1: Protein Factor VIIa (Heavy Chain) / Factor VII heavy chain / ACTIVATED FACTOR VIIA HEAVY CHAIN


Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: UNP residues 213-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa
#2: Protein Factor VIIa (Light Chain) / FACTOR VIIA LIGHT CHAIN


Mass: 6030.827 Da / Num. of mol.: 1 / Fragment: UKNP residues 150-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709

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Non-polymers , 5 types, 265 molecules

#3: Chemical ChemComp-2KE / (2R)-2-[(1-aminoisoquinolin-6-yl)amino]-2-[3-ethoxy-4-(propan-2-yloxy)phenyl]-N-(3-sulfamoylbenzyl)ethanamide


Mass: 563.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H33N5O5S
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 3.9 Å3/Da / Density % sol: 68.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, pH 6.0, 20 mM CACL2, 17.5%(W/V) PEG 6000, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 21, 2004 / Details: MICROMAX CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 28178 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Biso Wilson estimate: 31.58 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 27.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 5.6 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.11data extraction
HKL-2000(DENZO)data reduction
HKL-2000(SCALEPACK)data scaling
AMoREphasing
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DAN

1dan


Resolution: 2.2→19.89 Å / Cor.coef. Fo:Fc: 0.9392 / Cor.coef. Fo:Fc free: 0.9169 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.21 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 1161 4.79 %RANDOM
Rwork0.1853 ---
obs0.187 24216 86.5 %-
Displacement parametersBiso max: 114.85 Å2 / Biso mean: 30.8593 Å2 / Biso min: 10.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.7253 Å20 Å20 Å2
2--1.7253 Å20 Å2
3----3.4507 Å2
Refine analyzeLuzzati coordinate error obs: 0.245 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 72 257 2652
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d822SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes402HARMONIC5
X-RAY DIFFRACTIONt_it2496HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion316SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance6HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3046SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2496HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3412HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion15.54
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2616 141 4.95 %
Rwork0.2114 2706 -
all0.2139 2847 -
obs--86.5 %

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