Structure of PDB 5nar Chain A Binding Site BS01

Receptor Information
>5nar Chain A (length=217) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEGKVQVL
LGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPA
VRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATC
NTERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIY
TRVASYAAWIDSVLASA
Ligand information
Ligand ID8RW
InChIInChI=1S/C22H20F3N5O4/c23-22(24,25)34-14-6-3-5-13(11-14)27-19(31)18-9-4-10-29(18)21(33)28-16-12-30(20(26)32)17-8-2-1-7-15(16)17/h1-3,5-8,11-12,18H,4,9-10H2,(H2,26,32)(H,27,31)(H,28,33)/t18-/m0/s1
InChIKeyGPEWMCZCFCZAEI-SFHVURJKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc2c(c1)c(cn2C(=O)N)NC(=O)N3CCC[C@H]3C(=O)Nc4cccc(c4)OC(F)(F)F
CACTVS 3.385NC(=O)n1cc(NC(=O)N2CCC[C@H]2C(=O)Nc3cccc(OC(F)(F)F)c3)c4ccccc14
CACTVS 3.385NC(=O)n1cc(NC(=O)N2CCC[CH]2C(=O)Nc3cccc(OC(F)(F)F)c3)c4ccccc14
OpenEye OEToolkits 2.0.6c1ccc2c(c1)c(cn2C(=O)N)NC(=O)N3CCCC3C(=O)Nc4cccc(c4)OC(F)(F)F
FormulaC22 H20 F3 N5 O4
Name(2~{S})-~{N}1-(1-aminocarbonylindol-3-yl)-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide
ChEMBLCHEMBL3908849
DrugBank
ZINC
PDB chain5nar Chain A Residue 302 [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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PDB5nar Discovery of Highly Potent and Selective Small-Molecule Reversible Factor D Inhibitors Demonstrating Alternative Complement Pathway Inhibition in Vivo.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		H40 L41 C42 R151 C191 K192 G193 S195 T214 S215 G216 S217 R218 C220
Binding residue
(residue number reindexed from 1)		H24 L25 C26 R133 C166 K167 G168 S170 T185 S186 G187 S188 R189 C191
Annotation score1
Binding affinityMOAD: ic50=0.5uM
PDBbind-CN: -logKd/Ki=6.30,IC50=0.50uM
BindingDB: IC50=500nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 K192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H41 D85 K167 G168 D169 S170 G171
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:5nar, PDBe:5nar, PDBj:5nar
PDBsum5nar
PubMed28621538
UniProtP00746|CFAD_HUMAN Complement factor D (Gene Name=CFD)

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