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- PDB-7v18: Factor XIa in Complex with Compound 3f -

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Basic information

Entry
Database: PDB / ID: 7v18
TitleFactor XIa in Complex with Compound 3f
ComponentsCoagulation factor XIa light chain
KeywordsBLOOD CLOTTING / Hydrolase / SERINE PROTEASE / COAGULATION FACTOR
Function / homology
Function and homology information


coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 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 ...Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 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
CITRIC ACID / Chem-OTX / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.732 Å
AuthorsShaffer, P.L. / Milligan, C.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of Potent and Orally Bioavailable Pyridine N-Oxide-Based Factor XIa Inhibitors through Exploiting Nonclassical Interactions.
Authors: Xu, G. / Liu, Z. / Wang, X. / Lu, T. / DesJarlais, R.L. / Thieu, T. / Zhang, J. / Devine, Z.H. / Du, F. / Li, Q. / Milligan, C.M. / Shaffer, P. / Cedervall, P.E. / Spurlino, J.C. / Stratton, ...Authors: Xu, G. / Liu, Z. / Wang, X. / Lu, T. / DesJarlais, R.L. / Thieu, T. / Zhang, J. / Devine, Z.H. / Du, F. / Li, Q. / Milligan, C.M. / Shaffer, P. / Cedervall, P.E. / Spurlino, J.C. / Stratton, C.F. / Pietrak, B. / Szewczuk, L.M. / Wong, V. / Steele, R.A. / Bruinzeel, W. / Chintala, M. / Silva, J. / Gaul, M.D. / Macielag, M.J. / Nargund, R.
History
DepositionMay 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor XIa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6293
Polymers26,8561
Non-polymers7722
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.500, 59.790, 66.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coagulation factor XIa light chain / FXI / Plasma thromboplastin antecedent / PTA


Mass: 26856.496 Da / Num. of mol.: 1 / Mutation: C500S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Komagataella pastoris (fungus) / References: UniProt: P03951, coagulation factor XIa
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-OTX / 2-[(1~{R})-3-[bis(fluoranyl)methoxy]-1-[4-(3-methyl-1,2,3-triazol-4-yl)pyrazol-1-yl]propyl]-5-[3-chloranyl-6-(4-chloranyl-1,2,3-triazol-1-yl)-2-fluoranyl-phenyl]-1-oxidanyl-pyridine


Mass: 580.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H18Cl2F3N9O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 24% PEG 4000, 100mM Na Citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.732→35.42 Å / Num. obs: 22924 / % possible obs: 91.87 % / Redundancy: 6 % / Biso Wilson estimate: 33.01 Å2 / Rpim(I) all: 0.02 / Rrim(I) all: 0.049 / Net I/σ(I): 17.8
Reflection shellResolution: 1.732→1.794 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2447 / CC1/2: 0.87 / Rpim(I) all: 0.309 / Rrim(I) all: 0.801 / % possible all: 99.84

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Processing

Software
NameVersionClassification
PHENIX1.1refinement
PDB_EXTRACT3.27data extraction
autoPROC1.1.7data reduction
autoPROC1.1.7data scaling
PHENIX1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SOS

3sos


Resolution: 1.732→35.418 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 1097 4.79 %
Rwork0.1707 21820 -
obs0.1726 22917 91.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.67 Å2 / Biso mean: 43.5588 Å2 / Biso min: 22.58 Å2
Refinement stepCycle: final / Resolution: 1.732→35.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 52 71 1986
Biso mean--49.34 44.46 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062001
X-RAY DIFFRACTIONf_angle_d0.8512731
X-RAY DIFFRACTIONf_chiral_restr0.058286
X-RAY DIFFRACTIONf_plane_restr0.005359
X-RAY DIFFRACTIONf_dihedral_angle_d16.4111163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7322-1.8110.24641300.23012932100
1.811-1.90650.24581290.2181269292
1.9065-2.02590.23681260.1831251486
2.0259-2.18230.20161230.1856251486
2.1823-2.40190.22731240.1833230178
2.4019-2.74930.24611610.1911288098
2.7493-3.46340.20471490.1774296399
3.4634-35.4180.18671550.1506302497
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)
15.1006-2.3329-0.8622.7095-0.06522.673-0.2973-1.20540.38280.69360.27550.0988-0.0180.0023-0.03230.38780.05740.0310.50430.03190.270675.060867.349525.7518
22.66910.20360.05263.76770.63892.74-0.1559-0.19530.46190.2330.0791-0.2026-0.2587-0.08530.11340.22710.0116-0.03490.223-0.02550.233581.737777.84713.9214
34.43710.52660.79214.12820.16775.2275-0.1350.04020.2917-0.0980.0926-0.2503-0.30370.1315-0.06030.25350.02860.00960.18410.04760.329283.94676.95119.3963
45.3729-0.69690.40395.8161-0.32334.04630.0888-0.00640.165-0.0208-0.0535-0.5430.03820.1828-0.03660.2678-0.0334-0.00160.20380.02730.199682.500971.25966.9729
57.1122-0.3765-2.02293.9617-1.19613.12-0.22390.1981-0.8136-0.02380.20710.08390.6106-0.1559-0.04330.38340.0063-0.05570.29680.03260.297678.106558.426315.94
63.13250.871.38685.95270.22573.5124-0.2471-0.63830.50750.44990.21421.0524-0.4937-0.39540.08240.36930.0920.04860.48030.01650.42966.855672.581521.638
77.7516-1.4443-0.91015.96940.19376.37040.36010.106-0.7654-0.18550.01720.48080.4111-0.6705-0.35150.3174-0.054-0.10110.30770.06710.408259.348763.29172.5686
83.41230.6055-0.94581.96980.01431.69870.0096-0.40390.18040.16940.04550.6880.0762-0.436-0.07720.35010.0091-0.00610.40330.06890.410362.698967.185615.549
94.4906-2.01470.37286.1293-1.23193.8848-0.1015-0.3971-0.54550.03930.43050.28320.5509-0.2817-0.27140.2753-0.0142-0.040.25960.05870.259974.185759.8315.1318
108.98573.2650.78661.74372.11769.028-0.2873-0.3410.3745-0.1631-0.39471.314-0.5471-1.29140.28460.33420.0479-0.01590.5052-0.03160.640355.998569.760813.0449
112.3352-1.5732-1.32964.37440.88074.73280.11870.3972-0.3248-0.41770.0019-0.06920.28790.25-0.13480.3144-0.0104-0.0240.2932-0.02570.198778.758462.66363.2177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 388 through 401 )A388 - 401
2X-RAY DIFFRACTION2chain 'A' and (resid 402 through 453 )A402 - 453
3X-RAY DIFFRACTION3chain 'A' and (resid 454 through 474 )A454 - 474
4X-RAY DIFFRACTION4chain 'A' and (resid 475 through 491 )A475 - 491
5X-RAY DIFFRACTION5chain 'A' and (resid 492 through 518 )A492 - 518
6X-RAY DIFFRACTION6chain 'A' and (resid 519 through 541 )A519 - 541
7X-RAY DIFFRACTION7chain 'A' and (resid 542 through 557 )A542 - 557
8X-RAY DIFFRACTION8chain 'A' and (resid 558 through 577 )A558 - 577
9X-RAY DIFFRACTION9chain 'A' and (resid 578 through 595 )A578 - 595
10X-RAY DIFFRACTION10chain 'A' and (resid 596 through 605 )A596 - 605
11X-RAY DIFFRACTION11chain 'A' and (resid 606 through 623 )A606 - 623

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