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- PDB-5nat: Complement factor D in complex with the inhibitor (S)-Pyrrolidine... -

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Basic information

Entry
Database: PDB / ID: 5nat
TitleComplement factor D in complex with the inhibitor (S)-Pyrrolidine-1,2-dicarboxylic acid 1-[(1-methyl-1H-indol-3-yl)-amide] 2-[(3-trifluoromethoxy-phenyl)-amide]
ComponentsComplement factor DFactor D
KeywordsHYDROLASE
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-8RT / Complement factor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsMac Sweeney, A. / Ostermann, N.
CitationJournal: J.Med.Chem. / Year: 2017
Title: Discovery of Highly Potent and Selective Small-Molecule Reversible Factor D Inhibitors Demonstrating Alternative Complement Pathway Inhibition in Vivo.
Authors: Lorthiois, E. / Anderson, K. / Vulpetti, A. / Rogel, O. / Cumin, F. / Ostermann, N. / Steinbacher, S. / Mac Sweeney, A. / Delgado, O. / Liao, S.M. / Randl, S. / Rudisser, S. / Dussauge, S. / ...Authors: Lorthiois, E. / Anderson, K. / Vulpetti, A. / Rogel, O. / Cumin, F. / Ostermann, N. / Steinbacher, S. / Mac Sweeney, A. / Delgado, O. / Liao, S.M. / Randl, S. / Rudisser, S. / Dussauge, S. / Fettis, K. / Kieffer, L. / de Erkenez, A. / Yang, L. / Hartwieg, C. / Argikar, U.A. / La Bonte, L.R. / Newton, R. / Kansara, V. / Flohr, S. / Hommel, U. / Jaffee, B. / Maibaum, J.
History
DepositionFeb 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3704
Polymers24,7391
Non-polymers6313
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-2 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.438, 49.676, 55.562
Angle α, β, γ (deg.)90.00, 106.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24739.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00746, complement factor D
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-8RT / (2~{S})-~{N}1-(1-methylindol-3-yl)-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide


Mass: 446.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21F3N4O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: MM NACL + 1 UL RESERVOIR SOLUTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.17→53.42 Å / Num. obs: 64856 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 3.19 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 15.21
Reflection shellResolution: 1.17→1.22 Å / Redundancy: 1.88 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 3.6 / % possible all: 73.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
CNXphasing
REFMAC5.5.0063refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.17→37.9 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs61837 94.2 %
Refinement stepCycle: LAST / Resolution: 1.17→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 0 44 261 2017

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