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- PDB-7v16: Factor XIa in Complex with Compound 2j -

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Basic information

Entry
Database: PDB / ID: 7v16
TitleFactor XIa in Complex with Compound 2j
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. ...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 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
CITRIC ACID / Chem-OT7 / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.505 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

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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)27,5553
Polymers26,8561
Non-polymers6982
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.230, 59.880, 67.000
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-OT7 / 5-[3-chloranyl-2-fluoranyl-6-(1,2,3,4-tetrazol-1-yl)phenyl]-2-[(1~{R})-2-cyclopropyl-1-[4-(2-methylpyrazol-3-yl)pyrazol-1-yl]ethyl]-1-oxidanyl-pyridine


Mass: 505.935 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21ClFN9O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.39 %
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: Jul 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.505→35.653 Å / Num. obs: 38036 / % possible obs: 98.86 % / Redundancy: 6.5 % / Biso Wilson estimate: 21.91 Å2 / Rpim(I) all: 0.025 / Rrim(I) all: 0.059 / Net I/σ(I): 16.4
Reflection shellResolution: 1.505→1.559 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3729 / CC1/2: 0.72 / Rpim(I) all: 0.391 / Rrim(I) all: 0.995 / % possible all: 98.03

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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: 1.505→35.653 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1942 1961 5.16 %
Rwork0.1658 36072 -
obs0.1672 38033 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.36 Å2 / Biso mean: 30.1471 Å2 / Biso min: 15.08 Å2
Refinement stepCycle: final / Resolution: 1.505→35.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 49 152 2070
Biso mean--30.03 38.04 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052017
X-RAY DIFFRACTIONf_angle_d0.8012751
X-RAY DIFFRACTIONf_chiral_restr0.058287
X-RAY DIFFRACTIONf_plane_restr0.005361
X-RAY DIFFRACTIONf_dihedral_angle_d16.4181179
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.505-1.54270.25531430.2462250198
1.5427-1.58440.24071440.2188250098
1.5844-1.6310.22911430.2024254098
1.631-1.68370.20011240.1893254599
1.6837-1.74380.20161460.1793252799
1.7438-1.81360.20851640.1788250398
1.8136-1.89620.20231130.1658258099
1.8962-1.99610.16871600.1599253999
1.9961-2.12120.17231620.1599255199
2.1212-2.28490.18871360.1679259899
2.2849-2.51480.22461120.1707261099
2.5148-2.87860.19241370.17322641100
2.8786-3.62620.17291360.1591265199
3.6262-35.6530.20121410.15292786100
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)
13.4277-4.0070.95895.67460.98095.6564-0.0874-0.68290.16590.54470.1026-0.00530.07970.07720.03960.254-0.02510.00620.2579-0.01720.1337-16.8913-7.664725.6122
21.805-0.01820.0563.85460.16331.33320.009-0.0611-0.21860.2033-0.00360.10550.12480.052-0.00660.1656-0.00250.01350.16480.0140.1921-23.7578-17.969713.8791
34.57052.0881-2.31283.4396-2.53233.6528-0.1260.2216-0.1213-0.02790.20150.20590.1619-0.2813-0.06460.17560.02090.01430.1166-0.030.2037-25.7903-17.12769.4839
47.18470.5853-2.44473.37440.05234.4194-0.06880.17070.09870.04780.01570.26590.1147-0.15140.01350.13770.0091-0.01480.093-0.01250.1111-24.6134-11.3426.9818
57.32970.03851.33853.5849-0.06681.5663-0.04580.05990.8285-0.11230.06570.0349-0.29720.1973-0.05180.2792-0.01370.03850.1845-0.03880.2237-20.08111.637715.7643
62.39521.4816-0.82914.114-0.77993.56030.0219-0.4744-0.33570.2847-0.0642-0.58820.43160.39650.04020.25310.0522-0.06850.3450.01090.2577-9.2424-12.556321.2445
72.2839-2.9417-0.1524.2523-1.70148.61650.1592-0.00680.31670.04490.0375-0.2802-0.31890.5471-0.09170.1795-0.05780.02450.2243-0.05090.2574-0.9502-3.70552.2373
85.41710.3131.65012.4699-1.29844.60.0607-0.3781-0.02610.1515-0.1556-0.4014-0.12210.59530.0830.19390.0191-0.01670.2878-0.06320.2064-4.7861-7.5115.303
94.8287-4.33-1.73228.20483.27674.5940.0047-0.25980.46930.07130.2221-0.2783-0.34030.1707-0.22420.1561-0.02850.02020.1594-0.02810.2052-16.12360.041915.0399
102.78264.1134-1.79046.6068-2.14696.1045-0.0246-0.5629-0.54350.3226-0.2806-0.94280.15370.82160.21740.18020.0361-0.04260.3873-0.00180.37511.9835-10.12412.6442
118.0808-3.15635.37385.8528-2.49297.75850.06940.06250.2597-0.2759-0.02840.1573-0.1293-0.24060.0290.151-0.00520.03170.12950.00110.1147-20.8624-2.77113.1812
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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