Structure of PDB 5nba Chain A Binding Site BS01

Receptor Information
>5nba Chain A (length=225) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEKVQVLL
GAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAV
RPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCN
RRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCG
NRKKPGIYTRVASYAAWIDSVLASA
Ligand information
Ligand ID8S5
InChIInChI=1S/C22H19F4N5O4/c23-12-8-18(19(32)28-13-4-3-5-14(9-13)35-22(24,25)26)31(10-12)21(34)29-16-11-30(20(27)33)17-7-2-1-6-15(16)17/h1-7,9,11-12,18H,8,10H2,(H2,27,33)(H,28,32)(H,29,34)/t12-,18+/m1/s1
InChIKeyPFNAXJGGZUYQGP-XIKOKIGWSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC(=O)n1cc(NC(=O)N2C[CH](F)C[CH]2C(=O)Nc3cccc(OC(F)(F)F)c3)c4ccccc14
OpenEye OEToolkits 2.0.6c1ccc2c(c1)c(cn2C(=O)N)NC(=O)N3C[C@@H](C[C@H]3C(=O)Nc4cccc(c4)OC(F)(F)F)F
CACTVS 3.385NC(=O)n1cc(NC(=O)N2C[C@H](F)C[C@H]2C(=O)Nc3cccc(OC(F)(F)F)c3)c4ccccc14
OpenEye OEToolkits 2.0.6c1ccc2c(c1)c(cn2C(=O)N)NC(=O)N3CC(CC3C(=O)Nc4cccc(c4)OC(F)(F)F)F
FormulaC22 H19 F4 N5 O4
Name(2~{S},4~{R})-~{N}1-(1-aminocarbonylindol-3-yl)-4-fluoranyl-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide
ChEMBLCHEMBL3668698
DrugBank
ZINCZINC000148345686
PDB chain5nba Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5nba Discovery of Highly Potent and Selective Small-Molecule Reversible Factor D Inhibitors Demonstrating Alternative Complement Pathway Inhibition in Vivo.
Resolution1.87 Å
Binding residue
(original residue number in PDB)		H40 L41 H57 C58 R151 C191 K192 G193 S195 T214 S215 G216 S217 R218 C220
Binding residue
(residue number reindexed from 1)		H24 L25 H41 C42 R132 C174 K175 G176 S178 T193 S194 G195 S196 R197 C199
Annotation score1
Binding affinityMOAD: ic50=0.05uM
PDBbind-CN: -logKd/Ki=7.30,IC50=0.05uM
BindingDB: IC50=50nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 K192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H41 D84 K175 G176 D177 S178 G179
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
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Cellular Component
External links
PDB RCSB:5nba, PDBe:5nba, PDBj:5nba
PDBsum5nba
PubMed28621538
UniProtP00746|CFAD_HUMAN Complement factor D (Gene Name=CFD)

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