Structure of PDB 6skd Chain A Binding Site BS01

Receptor Information
>6skd Chain A (length=222) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVHGGPCDKTSHPYQAALYTSGHLLCGGVLIHPLWVLTAAHCKKPNLQVF
LGKHNLGQQESSQEQSSVVRAVIHPDYDAASHDQDIMLLRLARPAKLSEL
IQPLPLERDCSAQTTSCHILGWGKTADGDFPDTIQCAYIHLVSREECEHA
YPGQITQNMLCAGDEKYGKDSCQGDSGGPLVCGDHLRGLVSWGNYPCGSK
EKPGVYTNVCRYTNWIQKTIQA
Ligand information
Ligand IDLH2
InChIInChI=1S/C16H18BN3O2/c18-16(19)11-5-7-13(8-6-11)20-10-14-9-12-3-1-2-4-15(12)17(21)22-14/h1-8,14,20-21H,9-10H2,(H3,18,19)/t14-/m0/s1
InChIKeyGGBMYYYFHLXGRH-AWEZNQCLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[H]/N=C(\c1ccc(cc1)NC[C@@H]2Cc3ccccc3B(O2)O)/N
OpenEye OEToolkits 2.0.7B1(c2ccccc2CC(O1)CNc3ccc(cc3)C(=N)N)O
CACTVS 3.385NC(=N)c1ccc(NC[CH]2Cc3ccccc3B(O)O2)cc1
CACTVS 3.385NC(=N)c1ccc(NC[C@@H]2Cc3ccccc3B(O)O2)cc1
FormulaC16 H18 B N3 O2
Name4-[[(3~{S})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]methylamino]benzenecarboximidamide
ChEMBL
DrugBank
ZINC
PDB chain6skd Chain A Residue 302 [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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PDB6skd Design and development of a series of borocycles as selective, covalent kallikrein 5 inhibitors.
Resolution2.26 Å
Binding residue
(original residue number in PDB)		L41 C42 H57 D189 S190 Q192 G193 S195 V213 W215 G216 N217
Binding residue
(residue number reindexed from 1)		L25 C26 H41 D170 S171 Q173 G174 S176 V190 W192 G193 N194
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.80,IC50=1585nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 Q192 G193 D194 S195
Catalytic site (residue number reindexed from 1) H41 D85 Q173 G174 D175 S176
Enzyme Commision number 3.4.21.-
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008236 serine-type peptidase activity
Biological Process
GO:0006508 proteolysis
GO:0007417 central nervous system development
GO:0009611 response to wounding
GO:0010975 regulation of neuron projection development
GO:0016540 protein autoprocessing
GO:0030574 collagen catabolic process
GO:0042246 tissue regeneration
GO:0042445 hormone metabolic process
GO:0042552 myelination
GO:0042982 amyloid precursor protein metabolic process
GO:0045595 regulation of cell differentiation
GO:0045745 positive regulation of G protein-coupled receptor signaling pathway
Cellular Component
GO:0001533 cornified envelope
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum
GO:0030141 secretory granule
GO:0031965 nuclear membrane
GO:0045171 intercellular bridge

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6skd, PDBe:6skd, PDBj:6skd
PDBsum6skd
PubMed31521475
UniProtQ92876|KLK6_HUMAN Kallikrein-6 (Gene Name=KLK6)

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