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- PDB-4bvd: Identification of small molecule inhibitors selective for apo(a) ... -

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Basic information

Entry
Database: PDB / ID: 4bvd
TitleIdentification of small molecule inhibitors selective for apo(a) kringles KIV-7, KIV-10 and KV.
ComponentsAPOLIPOPROTEIN(A)
KeywordsHYDROLASE / CARDIOVASCULAR DISEASE / OPTICAL BIOSENSORS
Function / homology
Function and homology information


plasma lipoprotein particle / LDL remodeling / blood circulation / lipid transport / endopeptidase inhibitor activity / apolipoprotein binding / fibronectin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / lipid metabolic process / heparin binding ...plasma lipoprotein particle / LDL remodeling / blood circulation / lipid transport / endopeptidase inhibitor activity / apolipoprotein binding / fibronectin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / lipid metabolic process / heparin binding / endopeptidase activity / signaling receptor binding / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region
Similarity search - Function
Plasminogen Kringle 4 / Plasminogen Kringle 4 / : / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain ...Plasminogen Kringle 4 / Plasminogen Kringle 4 / : / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-BU6 / Apolipoprotein(a)
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsSandmark, J. / Althage, M. / Andersson, G.M.K. / Antonsson, T. / Blaho, S. / Bodin, C. / Bostrom, J. / Chen, Y. / Dahlen, A. / Eriksson, P.O. ...Sandmark, J. / Althage, M. / Andersson, G.M.K. / Antonsson, T. / Blaho, S. / Bodin, C. / Bostrom, J. / Chen, Y. / Dahlen, A. / Eriksson, P.O. / Evertsson, E. / Fex, T. / Fjellstrom, O. / Gustafsson, D. / Hallberg, C. / Hicks, R. / Jarkvist, E. / Johansson, C. / Kalies, I. / Kang, D. / Svalstedt Karlsson, B. / Kartberg, F. / Legnehed, A. / Lindqvist, A.M. / Martinsson, S.A. / Moberg, A. / Petersson, A.U. / Ridderstrom, M. / Thelin, A. / Tigerstrom, A. / Vinblad, J. / Xu, B. / Knecht, W.
CitationJournal: To be Published
Title: Small Molecules Used to Decipher the Pathophysiological Roles of the Kringle Domains Kiv-7, - 10 and Kv of Apolipoprotein(A)
Authors: Sandmark, J. / Althage, M. / Andersson, G.M.K. / Antonsson, T. / Blaho, S. / Bodin, C. / Bostrom, J. / Chen, Y. / Dahlen, A. / Eriksson, P.O. / Evertsson, E. / Fex, T. / Fjellstrom, O. / ...Authors: Sandmark, J. / Althage, M. / Andersson, G.M.K. / Antonsson, T. / Blaho, S. / Bodin, C. / Bostrom, J. / Chen, Y. / Dahlen, A. / Eriksson, P.O. / Evertsson, E. / Fex, T. / Fjellstrom, O. / Gustafsson, D. / Hallberg, C. / Hicks, R. / Jarkvist, E. / Johansson, C. / Kalies, I. / Kang, D. / Svalstedt Karlsson, B. / Kartberg, F. / Legnehed, A. / Lindqvist, A.M. / Martinsson, S.A. / Moberg, A. / Petersson, A.U. / Ridderstrom, M. / Thelin, A. / Tigerstrom, A. / Vinblad, J. / Xu, B. / Knecht, W.
History
DepositionJun 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: APOLIPOPROTEIN(A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5503
Polymers9,1561
Non-polymers3942
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.240, 45.270, 58.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein APOLIPOPROTEIN(A) / APO(A) / LP(A)


Mass: 9156.078 Da / Num. of mol.: 1 / Fragment: KRINGLE DOMAIN IV-10, RESIDUES 4123-4201 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZALPHAC / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): X-33
References: UniProt: P08519, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BU6 / 5-chloro-2-fluoro-N-[1-(4-piperidyl)pyrazol-4-yl]benzenesulfonamide


Mass: 358.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16ClFN4O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsKRINGLE IV-10 DOMAIN, N76A MUTATION

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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: 1.7 Å3/Da / Density % sol: 28 % / Description: NONE
Crystal growpH: 7.5 / Details: 25% PEG4000, 0.1M TRIS PH 8.5, 0.2 M CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.5418
DetectorType: RIGAKU A200-CU / Detector: CCD / Date: Feb 28, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→21 Å / Num. obs: 7776 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.1
Reflection shellResolution: 1.64→1.72 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 17.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KIV

3kiv


Resolution: 1.68→21.38 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21367 353 4.6 %RANDOM
Rwork0.17573 ---
obs0.1775 7363 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.683 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.62 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.68→21.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms629 0 24 104 757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.019690
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.948945
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.046579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55322.536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7731596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.971157
X-RAY DIFFRACTIONr_chiral_restr0.0920.289
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021577
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 24 -
Rwork0.25 544 -
obs--99.13 %

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