Structure of PDB 1kyn Chain A Binding Site BS01

Receptor Information
>1kyn Chain A (length=223) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IIGGRESRPHSRPYMAYLQIQSPAGQSRCGGFLVREDFVLTAAHCWGSNI
NVTLGAHNIQRRENTQQHITARRAIRHPQYNQRTIQNDIMLLQLSRRVRR
NRNVNPVALPRAQEGLRPGTLCTVAGWGRVSMRRGTDTLREVQLRVQRDR
QCLRIFGSYDPRRQICVGDRRERKAAFKGDSGGPLLCNNVAHGIVSYGKS
SGVPPEVFTRVSSFLPWIRTTMR
Ligand information
Ligand IDKTP
InChIInChI=1S/C22H17O4P/c23-21(18-13-12-15-6-1-2-8-17(15)14-18)22(27(24,25)26)20-11-5-9-16-7-3-4-10-19(16)20/h1-14,22H,(H2,24,25,26)/t22-/m1/s1
InChIKeyOFHMUASCSJJNNA-JOCHJYFZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc2cc(ccc2c1)C(=O)[C@@H](c3cccc4c3cccc4)P(=O)(O)O
OpenEye OEToolkits 1.5.0c1ccc2cc(ccc2c1)C(=O)C(c3cccc4c3cccc4)P(=O)(O)O
ACDLabs 10.04O=C(c2cc1ccccc1cc2)C(c4cccc3ccccc34)P(=O)(O)O
CACTVS 3.341O[P](O)(=O)[CH](C(=O)c1ccc2ccccc2c1)c3cccc4ccccc34
CACTVS 3.341O[P](O)(=O)[C@@H](C(=O)c1ccc2ccccc2c1)c3cccc4ccccc34
FormulaC22 H17 O4 P
Name(2-NAPHTHALEN-2-YL-1-NAPHTHALEN-1-YL-2-OXO-ETHYL)-PHOSPHONIC ACID;
BIS-NAPTHYL BETA-KETOPHOSPHONIC ACID
ChEMBL
DrugBankDB02360
ZINCZINC000002047839
PDB chain1kyn Chain A Residue 601 [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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PDB1kyn Nonpeptide inhibitors of cathepsin G: optimization of a novel beta-ketophosphonic acid lead by structure-based drug design.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		H57 A190 F191 K192 S195 G216 K217
Binding residue
(residue number reindexed from 1)		H44 A176 F177 K178 S181 G198 K199
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.39,IC50=4.1uM
BindingDB: IC50=4100nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 K192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H44 D88 K178 G179 D180 S181 G182
Enzyme Commision number 3.4.21.20: cathepsin G.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005515 protein binding
GO:0008201 heparin binding
GO:0008233 peptidase activity
GO:0008236 serine-type peptidase activity
GO:0048018 receptor ligand activity
GO:0089720 caspase binding
Biological Process
GO:0002003 angiotensin maturation
GO:0002548 monocyte chemotaxis
GO:0006468 protein phosphorylation
GO:0006508 proteolysis
GO:0006935 chemotaxis
GO:0006955 immune response
GO:0016485 protein processing
GO:0019221 cytokine-mediated signaling pathway
GO:0019731 antibacterial humoral response
GO:0022617 extracellular matrix disassembly
GO:0030168 platelet activation
GO:0032496 response to lipopolysaccharide
GO:0035590 purinergic nucleotide receptor signaling pathway
GO:0042119 neutrophil activation
GO:0042742 defense response to bacterium
GO:0050778 positive regulation of immune response
GO:0050829 defense response to Gram-negative bacterium
GO:0050830 defense response to Gram-positive bacterium
GO:0050832 defense response to fungus
GO:0050868 negative regulation of T cell activation
GO:0070946 neutrophil-mediated killing of gram-positive bacterium
GO:0071222 cellular response to lipopolysaccharide
GO:0098786 biofilm matrix disassembly
GO:1901731 positive regulation of platelet aggregation
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0010494 cytoplasmic stress granule
GO:0016020 membrane
GO:0030141 secretory granule
GO:0035578 azurophil granule lumen
GO:0043231 intracellular membrane-bounded organelle
GO:0062023 collagen-containing extracellular matrix
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1kyn, PDBe:1kyn, PDBj:1kyn
PDBsum1kyn
PubMed11942800
UniProtP08311|CATG_HUMAN Cathepsin G (Gene Name=CTSG)

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