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- PDB-6fug: Complement factor D in complex with the inhibitor 3-((3-((3-(amin... -

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Basic information

Entry
Database: PDB / ID: 6fug
TitleComplement factor D in complex with the inhibitor 3-((3-((3-(aminomethyl)phenyl)amino)-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino)phenol
ComponentsComplement factor D
KeywordsHYDROLASE / SERINE PROTEASE / inhibitor / complex
Function / homology
Function and homology information


complement factor D / Alternative complement activation / complement activation / complement activation, alternative pathway / serine-type peptidase activity / platelet alpha granule lumen / protein maturation / response to bacterium / Platelet degranulation / secretory granule lumen ...complement factor D / Alternative complement activation / complement activation / complement activation, alternative pathway / serine-type peptidase activity / platelet alpha granule lumen / protein maturation / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
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 ...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-E85 / Complement factor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsMac Sweeney, A. / Ostermann, N. / Vulpetti, A. / Maibaum, J. / Erbel, P. / Lorthiois, E. / Yoon, T. / Randl, S. / Ruedisser, S.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Discovery and Design of First Benzylamine-Based Ligands Binding to an Unlocked Conformation of the Complement Factor D.
Authors: Vulpetti, A. / Ostermann, N. / Randl, S. / Yoon, T. / Mac Sweeney, A. / Cumin, F. / Lorthiois, E. / Rudisser, S. / Erbel, P. / Maibaum, J.
History
DepositionFeb 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 2.0Nov 13, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Refinement description / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_polymer_linkage / struct_ncs_dom_lim
Item: _atom_site.label_seq_id / _database_2.pdbx_DOI ..._atom_site.label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_unobs_or_zero_occ_residues.PDB_ins_code / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement factor D
B: Complement factor D
C: Complement factor D
D: Complement factor D
E: Complement factor D
F: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,51912
Polymers148,4356
Non-polymers2,0846
Water5,134285
1
A: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0862
Polymers24,7391
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0862
Polymers24,7391
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0862
Polymers24,7391
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0862
Polymers24,7391
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0862
Polymers24,7391
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0862
Polymers24,7391
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.523, 68.482, 73.380
Angle α, β, γ (deg.)95.21, 116.70, 102.43
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA16 - 2431 - 228
21ALAALABB16 - 2431 - 228
12ALAALAAA16 - 2451 - 230
22ALAALACC16 - 2451 - 230
13ALAALAAA16 - 2451 - 230
23ALAALADD16 - 2451 - 230
14ALAALAAA16 - 2451 - 230
24ALAALAEE16 - 2451 - 230
15ALAALAAA16 - 2451 - 230
25ALAALAFF16 - 2451 - 230
16ALAALABB16 - 2431 - 228
26ALAALACC16 - 2431 - 228
17LEULEUBB16 - 2421 - 227
27LEULEUDD16 - 2421 - 227
18ALAALABB16 - 2431 - 228
28ALAALAEE16 - 2431 - 228
19ALAALABB16 - 2431 - 228
29ALAALAFF16 - 2431 - 228
110ALAALACC16 - 2451 - 230
210ALAALADD16 - 2451 - 230
111ALAALACC16 - 2451 - 230
211ALAALAEE16 - 2451 - 230
112ALAALACC16 - 2451 - 230
212ALAALAFF16 - 2451 - 230
113ALAALADD16 - 2451 - 230
213ALAALAEE16 - 2451 - 230
114ALAALADD16 - 2451 - 230
214ALAALAFF16 - 2451 - 230
115ALAALAEE16 - 2451 - 230
215ALAALAFF16 - 2451 - 230

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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


Mass: 24739.121 Da / Num. of mol.: 6
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-E85 / 3-[[3-[[3-(aminomethyl)phenyl]amino]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-yl]amino]phenol


Mass: 347.374 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H17N7O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG3350, 100 mM TRIS pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→50.8 Å / Num. obs: 52329 / % possible obs: 94.3 % / Redundancy: 2 % / Net I/σ(I): 13.3
Reflection shellResolution: 2.21→2.28 Å / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 3.33

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→46.11 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.687 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.531 / ESU R Free: 0.268 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25905 2617 5 %RANDOM
Rwork0.22127 ---
obs0.22316 49708 94.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.556 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.01 Å2-0.07 Å2
2--0.31 Å2-0.27 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.21→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9568 0 156 285 10009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910077
X-RAY DIFFRACTIONr_bond_other_d0.0030.029400
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.98713756
X-RAY DIFFRACTIONr_angle_other_deg1.017321714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99751301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83123.197391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.969151557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3641585
X-RAY DIFFRACTIONr_chiral_restr0.0850.21559
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111276
X-RAY DIFFRACTIONr_gen_planes_other0.010.021979
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_it3.4584.0945188
X-RAY DIFFRACTIONr_mcbond_other3.4584.0935187
X-RAY DIFFRACTIONr_mcangle_it5.2366.1126463
X-RAY DIFFRACTIONr_mcangle_other5.2356.1136464
X-RAY DIFFRACTIONr_scbond_it3.7454.5614889
X-RAY DIFFRACTIONr_scbond_other3.7444.564890
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7956.6577284
X-RAY DIFFRACTIONr_long_range_B_refined8.35648.38910551
X-RAY DIFFRACTIONr_long_range_B_other8.34848.37210523
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A127760.05
12B127760.05
21A130120.04
22C130120.04
31A129860.04
32D129860.04
41A128200.05
42E128200.05
51A128320.05
52F128320.05
61B129780.04
62C129780.04
71B130120.05
72D130120.05
81B129740.04
82E129740.04
91B129420.05
92F129420.05
101C129520.05
102D129520.05
111C127520.05
112E127520.05
121C127680.05
122F127680.05
131D129200.05
132E129200.05
141D129100.05
142F129100.05
151E130680.04
152F130680.04
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 193 -
Rwork0.281 3660 -
obs--94.3 %

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