Structure of PDB 5nb6 Chain A Binding Site BS01

Receptor Information
>5nb6 Chain A (length=216) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEGKVQVL
LGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPA
VRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATC
NERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYT
RVASYAAWIDSVLASA
Ligand information
Ligand ID8S2
InChIInChI=1S/C22H21F3N6O4/c23-22(24,25)35-14-5-3-4-13(9-14)28-19(32)18-8-12(26)10-31(18)21(34)29-16-11-30(20(27)33)17-7-2-1-6-15(16)17/h1-7,9,11-12,18H,8,10,26H2,(H2,27,33)(H,28,32)(H,29,34)/t12-,18-/m0/s1
InChIKeyBOUWILWEXWTKKH-SGTLLEGYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385N[C@H]1C[C@H](N(C1)C(=O)Nc2cn(C(N)=O)c3ccccc23)C(=O)Nc4cccc(OC(F)(F)F)c4
OpenEye OEToolkits 2.0.6c1ccc2c(c1)c(cn2C(=O)N)NC(=O)N3CC(CC3C(=O)Nc4cccc(c4)OC(F)(F)F)N
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)N
CACTVS 3.385N[CH]1C[CH](N(C1)C(=O)Nc2cn(C(N)=O)c3ccccc23)C(=O)Nc4cccc(OC(F)(F)F)c4
FormulaC22 H21 F3 N6 O4
Name(2~{S},4~{S})-~{N}1-(1-aminocarbonylindol-3-yl)-4-azanyl-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide
ChEMBLCHEMBL3673825
DrugBank
ZINCZINC000148384563
PDB chain5nb6 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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PDB5nb6 Discovery of Highly Potent and Selective Small-Molecule Reversible Factor D Inhibitors Demonstrating Alternative Complement Pathway Inhibition in Vivo.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		H40 L41 C42 R151 C191 K192 G193 S195 T214 S215 G216 R218
Binding residue
(residue number reindexed from 1)		H24 L25 C26 R133 C165 K166 G167 S169 T184 S185 G186 R188
Annotation score1
Binding affinityMOAD: ic50=0.5uM
PDBbind-CN: -logKd/Ki=6.30,IC50=0.50uM
BindingDB: IC50=667nM
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 K166 G167 D168 S169 G170
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:5nb6, PDBe:5nb6, PDBj:5nb6
PDBsum5nb6
PubMed28621538
UniProtP00746|CFAD_HUMAN Complement factor D (Gene Name=CFD)

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