Structure of PDB 5nat Chain A Binding Site BS01

Receptor Information
>5nat Chain A (length=228) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGK
VQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKAT
LGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLD
RATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSG
SRVCGNRKKPGIYTRVASYAAWIDSVLA
Ligand information
Ligand ID8RT
InChIInChI=1S/C22H21F3N4O3/c1-28-13-17(16-8-2-3-9-18(16)28)27-21(31)29-11-5-10-19(29)20(30)26-14-6-4-7-15(12-14)32-22(23,24)25/h2-4,6-9,12-13,19H,5,10-11H2,1H3,(H,26,30)(H,27,31)/t19-/m0/s1
InChIKeyIRTQBCRDCGFMII-IBGZPJMESA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cn1cc(NC(=O)N2CCC[C@H]2C(=O)Nc3cccc(OC(F)(F)F)c3)c4ccccc14
OpenEye OEToolkits 2.0.6Cn1cc(c2c1cccc2)NC(=O)N3CCC[C@H]3C(=O)Nc4cccc(c4)OC(F)(F)F
OpenEye OEToolkits 2.0.6Cn1cc(c2c1cccc2)NC(=O)N3CCCC3C(=O)Nc4cccc(c4)OC(F)(F)F
CACTVS 3.385Cn1cc(NC(=O)N2CCC[CH]2C(=O)Nc3cccc(OC(F)(F)F)c3)c4ccccc14
FormulaC22 H21 F3 N4 O3
Name(2~{S})-~{N}1-(1-methylindol-3-yl)-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide
ChEMBLCHEMBL4103449
DrugBank
ZINC
PDB chain5nat Chain A Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5nat Discovery of Highly Potent and Selective Small-Molecule Reversible Factor D Inhibitors Demonstrating Alternative Complement Pathway Inhibition in Vivo.
Resolution1.17 Å
Binding residue
(original residue number in PDB)		H40 L41 C42 H57 R151 C191 K192 G193 S195 S215 S217 R218
Binding residue
(residue number reindexed from 1)		H24 L25 C26 H41 R137 C179 K180 G181 S183 S199 S201 R202
Annotation score1
Binding affinityBindingDB: IC50=20000nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 K192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H41 D89 K180 G181 D182 S183 G184
Enzyme Commision number 3.4.21.46: complement factor D.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0008236 serine-type peptidase activity
Biological Process
GO:0006508 proteolysis
GO:0006956 complement activation
GO:0006957 complement activation, alternative pathway
GO:0009617 response to bacterium
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0031093 platelet alpha granule lumen
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5nat, PDBe:5nat, PDBj:5nat
PDBsum5nat
PubMed28621538
UniProtP00746|CFAD_HUMAN Complement factor D (Gene Name=CFD)

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