Structure of PDB 8dg6 Chain A Binding Site BS01

Receptor Information
>8dg6 Chain A (length=212) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ILGGREAEAHARPYMASVQNGAHLCGGVLVAEQWVLSAAHCLVQVLLGAH
SLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPL
PWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRTE
RLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRV
ASYAAWIDSVLA
Ligand information
Ligand IDS7X
InChIInChI=1S/C22H21ClFN5O3/c23-15-7-3-5-13(19(15)24)11-26-22(32)17-9-4-10-28(17)18(30)12-29-16-8-2-1-6-14(16)20(27-29)21(25)31/h1-3,5-8,17H,4,9-12H2,(H2,25,31)(H,26,32)/t17-/m0/s1
InChIKeyCNXBYALMVOPTMF-KRWDZBQOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc2c(c1)c(nn2CC(=O)N3CCCC3C(=O)NCc4cccc(c4F)Cl)C(=O)N
OpenEye OEToolkits 2.0.7c1ccc2c(c1)c(nn2CC(=O)N3CCC[C@H]3C(=O)NCc4cccc(c4F)Cl)C(=O)N
CACTVS 3.385NC(=O)c1nn(CC(=O)N2CCC[CH]2C(=O)NCc3cccc(Cl)c3F)c4ccccc14
CACTVS 3.385NC(=O)c1nn(CC(=O)N2CCC[C@H]2C(=O)NCc3cccc(Cl)c3F)c4ccccc14
ACDLabs 12.01Clc1cccc(CNC(=O)C2CCCN2C(=O)Cn2nc(c3ccccc32)C(N)=O)c1F
FormulaC22 H21 Cl F N5 O3
Name1-{2-[(2S)-2-{[(3-chloro-2-fluorophenyl)methyl]carbamoyl}pyrrolidin-1-yl]-2-oxoethyl}-1H-indazole-3-carboxamide
ChEMBLCHEMBL5219728
DrugBank
ZINC
PDB chain8dg6 Chain A Residue 301 [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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PDB8dg6 Scaffold hopping via ring opening enables identification of acyclic compounds as new complement Factor D inhibitors.
Resolution1.986 Å
Binding residue
(original residue number in PDB)		H24 L25 C26 H41 R137 C179 K180 G181 S183 T198 S199 G200 S201 R202
Binding residue
(residue number reindexed from 1)		H23 L24 C25 H40 R129 C163 K164 G165 S167 T182 S183 G184 S185 R186
Annotation score1
Enzymatic activity
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8dg6, PDBe:8dg6, PDBj:8dg6
PDBsum8dg6
PubMed36272185
UniProtP00746|CFAD_HUMAN Complement factor D (Gene Name=CFD)

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