Structure of PDB 6fty Chain A Binding Site BS01

Receptor Information
>6fty 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 IDE7H
InChIInChI=1S/C20H24N4O2/c21-17(25)16-5-13-14(23-16)2-1-3-15(13)24-18(26)19-6-11-4-12(7-19)9-20(22,8-11)10-19/h1-3,5,11-12,23H,4,6-10,22H2,(H2,21,25)(H,24,26)/t11-,12+,19+,20-
InChIKeyWGKDLQGKGXBCBV-SRRICDNISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc2c(cc([nH]2)C(=O)N)c(c1)NC(=O)C34C[C@H]5C[C@@H](C3)CC(C5)(C4)N
OpenEye OEToolkits 2.0.6c1cc2c(cc([nH]2)C(=O)N)c(c1)NC(=O)C34CC5CC(C3)CC(C5)(C4)N
CACTVS 3.385NC(=O)c1[nH]c2cccc(NC(=O)C34C[CH]5C[CH](CC(N)(C5)C3)C4)c2c1
CACTVS 3.385NC(=O)c1[nH]c2cccc(NC(=O)C34C[C@@H]5C[C@@H](CC(N)(C5)C3)C4)c2c1
FormulaC20 H24 N4 O2
Name4-[[(5~{S},7~{R})-3-azanyl-1-adamantyl]carbonylamino]-1~{H}-indole-2-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6fty 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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PDB6fty Discovery and Design of First Benzylamine-Based Ligands Binding to an Unlocked Conformation of the Complement Factor D.
Resolution1.67 Å
Binding residue
(original residue number in PDB)		L41 C42 H57 S190 C191 K192 S195 S215 S217 R218 C220
Binding residue
(residue number reindexed from 1)		L25 C26 H41 S178 C179 K180 S183 S199 S201 R202 C204
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=2.70,Kd>2000uM
BindingDB: Kd=>2000000nM
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:6fty, PDBe:6fty, PDBj:6fty
PDBsum6fty
PubMed29795765
UniProtP00746|CFAD_HUMAN Complement factor D (Gene Name=CFD)

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