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- PDB-7v12: Factor XIa in Complex with Compound 2f -

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Basic information

Entry
Database: PDB / ID: 7v12
TitleFactor XIa in Complex with Compound 2f
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-OR0 / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.631 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 1.3Oct 16, 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)27,5853
Polymers26,8561
Non-polymers7282
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.604, 59.627, 66.686
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-OR0 / 5-[1-[(1~{R})-1-[5-[3-chloranyl-2-fluoranyl-6-(1,2,3,4-tetrazol-1-yl)phenyl]-1-oxidanyl-pyridin-2-yl]-2-cyclopropyl-ethyl]pyrazol-4-yl]-6-fluoranyl-pyridin-2-amine


Mass: 535.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H20ClF2N9O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 25830 / % possible obs: 86.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.55 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.047 / Rrim(I) all: 0.097 / Χ2: 2.237 / Net I/σ(I): 10.2 / Num. measured all: 89404
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.63-1.662.40.84710070.5410.6381.0671.33968.2
1.66-1.692.60.71410280.5610.5230.891.27370.8
1.69-1.722.70.61510640.6820.4390.761.35372.2
1.72-1.762.70.55511000.7280.3970.6861.28474.4
1.76-1.792.70.45310930.7880.320.5581.28975
1.79-1.842.80.37411200.8580.2620.4591.37676.6
1.84-1.882.80.3511430.8810.2470.431.39677.9
1.88-1.932.80.28111920.8930.1970.3451.66680.3
1.93-1.992.90.2512310.9350.1720.3051.53583
1.99-2.052.90.21412510.9390.1470.2611.785.5
2.05-2.132.90.1813010.9470.1220.2181.98488
2.13-2.212.90.15613530.9640.1060.1891.85690.9
2.21-2.3130.14413620.9690.0960.1742.18392.5
2.31-2.433.20.12914670.9760.0840.1552.09697.9
2.43-2.593.40.11514650.9820.0730.1372.21699
2.59-2.793.70.10915020.9840.0640.1262.50299.3
2.79-3.074.40.09314980.9890.0490.1062.61499.2
3.07-3.515.30.07414850.9920.0350.0822.98598.3
3.51-4.425.80.06115390.9960.0280.0673.09599.7
4.42-505.10.05616290.9950.0270.0632.8199.3

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Processing

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

3sos


Resolution: 1.631→41.796 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2236 1982 7.69 %
Rwork0.1835 23804 -
obs0.1866 25786 86.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.63 Å2 / Biso mean: 21.6644 Å2 / Biso min: 6.92 Å2
Refinement stepCycle: final / Resolution: 1.631→41.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 76 112 2063
Biso mean--26.51 27.14 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091997
X-RAY DIFFRACTIONf_angle_d1.0092720
X-RAY DIFFRACTIONf_chiral_restr0.07284
X-RAY DIFFRACTIONf_plane_restr0.006356
X-RAY DIFFRACTIONf_dihedral_angle_d14.7951163
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6315-1.67230.34491080.3205134769
1.6723-1.71750.36311130.2701138873
1.7175-1.7680.31551260.2409142074
1.768-1.82510.23511130.2114147476
1.8251-1.89030.22191280.2032150978
1.8903-1.9660.251340.1922157581
1.966-2.05550.22011390.1832164985
2.0555-2.16390.2481380.1923173389
2.1639-2.29940.21921460.1866180092
2.2994-2.47690.24251660.1889191898
2.4769-2.72620.24631610.1891194699
2.7262-3.12050.21421670.1924196199
3.1205-3.93110.2081680.1582199099
3.9311-41.7960.18761750.1612094100
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)
10.9069-0.00350.18160.9960.27970.4463-0.0169-0.0224-0.11280.0634-0.00480.10490.1026-0.0005-0.00070.10440.0020.01750.10290.0040.0997-22.8504-15.410113.223
20.2395-0.08540.07720.08750.03060.0685-0.0536-0.04950.32340.05770.14490.0209-0.1536-0.02130.0020.1497-0.01590.02240.12430.00560.1614-19.58221.508615.7211
31.06540.0125-0.37760.50980.12120.85960.0565-0.09410.02680.02990.049-0.1254-0.040.15990.19580.08620.0010.00190.0995-0.01860.1004-9.0513-6.188411.9057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 388 through 491 )A388 - 491
2X-RAY DIFFRACTION2chain 'A' and (resid 492 through 518 )A492 - 518
3X-RAY DIFFRACTION3chain 'A' and (resid 519 through 623 )A519 - 623

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