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- PDB-7v0z: Factor XIa in Complex with Compound 2a -

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Basic information

Entry
Database: PDB / ID: 7v0z
TitleFactor XIa in Complex with Compound 2a
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
Chem-OQ6 / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShaffer, P.L. / Spurlino, J. / 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 1.3Nov 13, 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

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Assembly

Deposited unit
A: Coagulation factor XIa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4132
Polymers26,8561
Non-polymers5571
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.825, 59.690, 67.244
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-OQ6 / methyl ~{N}-[4-[1-[(1~{R})-1-[5-[5-chloranyl-2-(1,2,3,4-tetrazol-1-yl)phenyl]-1-oxidanyl-pyridin-2-yl]-2-cyclopropyl-ethyl]pyrazol-4-yl]phenyl]carbamate


Mass: 557.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H25ClN8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.24 Å3/Da / Density % sol: 44.97 %
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: Mar 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 23034 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 22.81 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.042 / Rrim(I) all: 0.106 / Χ2: 1.322 / Net I/σ(I): 6.5 / Num. measured all: 143942
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8350.70711220.70.3510.7920.5899.8
1.83-1.865.80.61311260.8140.2760.6740.608100
1.86-1.96.40.52711110.8650.2250.5740.695100
1.9-1.946.40.4511630.8850.1920.490.757100
1.94-1.986.40.40211080.8970.1710.4380.88100
1.98-2.036.30.33611290.9240.1440.3660.929100
2.03-2.086.10.29511570.9330.1310.3231.037100
2.08-2.136.30.26211420.9440.1130.2851.186100
2.13-2.26.40.22111410.9620.0940.2411.273100
2.2-2.276.60.19711220.9670.0830.2141.322100
2.27-2.356.50.16311420.9780.0690.1781.381100
2.35-2.446.30.15711390.9830.0670.1711.41699.9
2.44-2.556.20.14111450.9790.0620.1541.57199.9
2.55-2.696.30.12211480.9860.0530.1331.686100
2.69-2.866.60.10811640.9870.0460.1171.689100
2.86-3.086.50.09311510.9920.0390.1011.847100
3.08-3.396.20.07611760.9920.0330.0831.951100
3.39-3.886.50.06711730.9950.0280.0732.031100
3.88-4.886.10.05711960.9960.0250.0631.847100
4.88-505.80.04712790.9970.0210.0511.3899.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.19.2.4158refinement
PDB_EXTRACT3.27data extraction
PHENIX1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SOS

3sos


Resolution: 1.8→44.7 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 1991 8.66 %
Rwork0.1761 20989 -
obs0.1784 22980 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.9 Å2 / Biso mean: 27.6547 Å2 / Biso min: 11.73 Å2
Refinement stepCycle: final / Resolution: 1.8→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 40 69 1989
Biso mean--28.5 29.56 -
Num. residues----237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.33081320.27591386151893
1.84-1.890.28171410.218414731614100
1.89-1.950.2051390.188714691608100
1.95-2.010.20651420.171514891631100
2.01-2.080.20391410.173414851626100
2.08-2.160.23091420.189214951637100
2.16-2.260.23391410.202714911632100
2.26-2.380.21221410.179314881629100
2.38-2.530.20791440.186714991643100
2.53-2.730.20531430.183415211664100
2.73-30.26671410.19815191660100
3-3.430.19411410.170215051646100
3.44-4.330.1761480.15115501698100
4.33-44.70.15681550.158316191774100
Refinement TLS params.Method: refined / Origin x: 24.2428 Å / Origin y: -1.9126 Å / Origin z: -3.8433 Å
111213212223313233
T0.1337 Å2-0.0065 Å20.0063 Å2-0.1394 Å2-0.0101 Å2--0.1059 Å2
L1.6362 °2-0.3076 °2-0.1582 °2-2.0625 °2-0.3844 °2--1.0639 °2
S0.0233 Å °-0.143 Å °0.0321 Å °0.1078 Å °0.0245 Å °-0.0033 Å °-0.0713 Å °0.0143 Å °-0.0303 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 388 through 624)

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