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- PDB-6qmt: Complement factor D in complex with the inhibitor 2-(2-(3'-(amino... -

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Basic information

Entry
Database: PDB / ID: 6qmt
TitleComplement factor D in complex with the inhibitor 2-(2-(3'-(aminomethyl)-[1,1'-biphenyl]-3-carboxamido)phenyl)acetic acid
ComponentsComplement factor DFactor D
KeywordsHYDROLASE / Complement factor D / inhibitor
Function / homology
Function and homology information


complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen ...complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular exosome / extracellular region
Similarity search - Function
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 / Trypsin-like serine proteases ...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 / 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-J7B / Complement factor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKarki, R. / Powers, J. / Mainolfi, N. / Anderson, K. / Belanger, D. / Liu, D. / Jendza, K. / Gelin, C.F. / Solovay, C. / Mac Sweeeny, A. ...Karki, R. / Powers, J. / Mainolfi, N. / Anderson, K. / Belanger, D. / Liu, D. / Jendza, K. / Gelin, C.F. / Solovay, C. / Mac Sweeeny, A. / Delgado, O. / Crowley, M. / Liao, S.-M. / Argikar, U.A. / Flohr, S. / La Bonte, L.R. / Lorthiois, E.L. / Vulpetti, A. / Cumin, F. / Brown, A. / Adams, C. / Jaffee, B. / Mogi, M.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Design, Synthesis, and Preclinical Characterization of Selective Factor D Inhibitors Targeting the Alternative Complement Pathway.
Authors: Karki, R.G. / Powers, J. / Mainolfi, N. / Anderson, K. / Belanger, D.B. / Liu, D. / Ji, N. / Jendza, K. / Gelin, C.F. / Mac Sweeney, A. / Solovay, C. / Delgado, O. / Crowley, M. / Liao, S.M. ...Authors: Karki, R.G. / Powers, J. / Mainolfi, N. / Anderson, K. / Belanger, D.B. / Liu, D. / Ji, N. / Jendza, K. / Gelin, C.F. / Mac Sweeney, A. / Solovay, C. / Delgado, O. / Crowley, M. / Liao, S.M. / Argikar, U.A. / Flohr, S. / La Bonte, L.R. / Lorthiois, E.L. / Vulpetti, A. / Brown, A. / Long, D. / Prentiss, M. / Gradoux, N. / de Erkenez, A. / Cumin, F. / Adams, C. / Jaffee, B. / Mogi, M.
History
DepositionFeb 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2May 22, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement factor D
B: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9174
Polymers54,1962
Non-polymers7212
Water1,60389
1
A: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4582
Polymers27,0981
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4582
Polymers27,0981
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.964, 39.235, 63.502
Angle α, β, γ (deg.)83.030, 75.340, 65.170
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Complement factor D / Factor D / Adipsin / C3 convertase activator / Properdin factor D


Mass: 27097.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFD, DF, PFD / Production host: Escherichia coli (E. coli) / References: UniProt: P00746, complement factor D
#2: Chemical ChemComp-J7B / 2-[2-[[3-[3-(aminomethyl)phenyl]phenyl]carbonylamino]phenyl]ethanoic acid


Mass: 360.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H20N2O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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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: 1.71 Å3/Da / Density % sol: 28.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEGME 3350, 100 mM Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→61.41 Å / Num. obs: 37403 / % possible obs: 92.9 % / Observed criterion σ(F): -3 / Redundancy: 2.35 % / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.063 / Net I/σ(I): 10.93
Reflection shellResolution: 1.63→1.73 Å / Redundancy: 2.15 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 5507 / Rrim(I) all: 0.4 / % possible all: 84.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DSU

1dsu


Resolution: 1.8→35.6 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.158
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 1414 5 %RANDOM
Rwork0.202 ---
obs0.2035 26852 94.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.8 Å2 / Biso mean: 25.871 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20.04 Å2-0.03 Å2
2--0.13 Å20.06 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.8→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 54 90 3506
Biso mean--16.5 26.83 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133589
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173321
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.6544902
X-RAY DIFFRACTIONr_angle_other_deg2.4961.5817693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3915475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83820.562178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.05215559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9761534
X-RAY DIFFRACTIONr_chiral_restr0.1460.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024096
X-RAY DIFFRACTIONr_gen_planes_other0.010.02720
X-RAY DIFFRACTIONr_mcbond_it3.472.4551852
X-RAY DIFFRACTIONr_mcbond_other3.2832.4521851
X-RAY DIFFRACTIONr_mcangle_it4.2833.6132310
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 101 -
Rwork0.255 1923 -
all-2024 -
obs--94.23 %

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