Structure of PDB 5tcc Chain G Binding Site BS01

Receptor Information
>5tcc Chain G (length=226) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDDGKVQ
VLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLG
PAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRA
TCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSR
VCGNRKKPGIYTRVASYAAWIDSVLA
Ligand information
Ligand IDJ56
InChIInChI=1S/C18H16BrN5O2S/c19-14-6-3-7-15(21-14)22-17(26)18-23(8-9-27-18)16(25)11-24-13-5-2-1-4-12(13)10-20-24/h1-7,10,18H,8-9,11H2,(H,21,22,26)/t18-/m0/s1
InChIKeyJSZBVXMPHMCOIC-SFHVURJKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Brc1cccc(NC(=O)[C@@H]2SCCN2C(=O)Cn3ncc4ccccc34)n1
OpenEye OEToolkits 2.0.6c1ccc2c(c1)cnn2CC(=O)N3CCSC3C(=O)Nc4cccc(n4)Br
OpenEye OEToolkits 2.0.6c1ccc2c(c1)cnn2CC(=O)N3CCS[C@H]3C(=O)Nc4cccc(n4)Br
CACTVS 3.385Brc1cccc(NC(=O)[CH]2SCCN2C(=O)Cn3ncc4ccccc34)n1
ACDLabs 12.01O=C(C1SCCN1C(=O)Cn3c2ccccc2cn3)Nc4nc(ccc4)Br
FormulaC18 H16 Br N5 O2 S
Name(2S)-N-(6-bromopyridin-2-yl)-3-[(1H-indazol-1-yl)acetyl]-1,3-thiazolidine-2-carboxamide
ChEMBLCHEMBL3924715
DrugBank
ZINCZINC000584905602
PDB chain5tcc Chain G Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5tcc Buried Hydrogen Bond Interactions Contribute to the High Potency of Complement Factor D Inhibitors.
Resolution3.37 Å
Binding residue
(original residue number in PDB)		L40 C41 H56 C57 R152 K195 G196 S198 S214 G215 S216 R217
Binding residue
(residue number reindexed from 1)		L25 C26 H41 C42 R135 K178 G179 S181 S197 G198 S199 R200
Annotation score1
Binding affinityBindingDB: IC50=77nM,Kd=2210nM
Enzymatic activity
Catalytic site (original residue number in PDB) H56 D104 K195 G196 D197 S198 G199
Catalytic site (residue number reindexed from 1) H41 D87 K178 G179 D180 S181 G182
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:5tcc, PDBe:5tcc, PDBj:5tcc
PDBsum5tcc
PubMed27994744
UniProtP00746|CFAD_HUMAN Complement factor D (Gene Name=CFD)

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