Structure of PDB 5y9l Chain A Binding Site BS01

Receptor Information
>5y9l Chain A (length=224) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IIDGAPCARGSHPWQVALLSGNQLHCGGVLVNERWVLTAAHCKMNEYTVH
LGSDTLGDRRAQRIKASKSFRHPGYSTQTHVNDLMLVKLNSQARLSSMVK
KVRLPSRCEPPGTTCTVSGWGTTTSPDVTFPSDLMCVDVKLISPQDCTKV
YKDLLENSMLCAGIPDSKKNACNGDSGGPLVCRGTLQGLVSWGTFPCGQP
NDPGVYTQVCKFTKWINDTMKKHR
Ligand information
Ligand ID8R3
InChIInChI=1S/C24H28ClN5O5/c1-29(2)28-21-13-30(14-22(31)27-19-6-4-5-15(11-19)24(33)34)23(32)17(12-26-21)9-16-10-18(25)7-8-20(16)35-3/h4-8,10-11,17H,9,12-14H2,1-3H3,(H,26,28)(H,27,31)(H,33,34)/t17-/m1/s1
InChIKeySTRUTOBZXDUGAL-QGZVFWFLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CN(C)N=C1CN(C(=O)C(CN1)Cc2cc(ccc2OC)Cl)CC(=O)Nc3cccc(c3)C(=O)O
OpenEye OEToolkits 2.0.6CN(C)/N=C\1/CN(C(=O)[C@@H](CN1)Cc2cc(ccc2OC)Cl)CC(=O)Nc3cccc(c3)C(=O)O
CACTVS 3.385COc1ccc(Cl)cc1C[CH]2CNC(CN(CC(=O)Nc3cccc(c3)C(O)=O)C2=O)=NN(C)C
CACTVS 3.385COc1ccc(Cl)cc1C[C@@H]2CNC(/CN(CC(=O)Nc3cccc(c3)C(O)=O)C2=O)=N\N(C)C
FormulaC24 H28 Cl N5 O5
Name3-[2-[(3Z,6R)-6-[(5-chloranyl-2-methoxy-phenyl)methyl]-3-(dimethylhydrazinylidene)-7-oxidanylidene-1,4-diazepan-1-yl]ethanoylamino]benzoic acid
ChEMBLCHEMBL4302033
DrugBank
ZINC
PDB chain5y9l 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5y9l Discovery and structure-activity relationship study of 1,3,6-trisubstituted 1,4-diazepane-7-ones as novel human kallikrein 7 inhibitors
Resolution2.15 Å
Binding residue
(original residue number in PDB)		H57 H99 F151 A190 C191 N192 S195 S214 W215 G216 C220
Binding residue
(residue number reindexed from 1)		H41 H80 F130 A171 C172 N173 S176 S191 W192 G193 C197
Annotation score1
Binding affinityMOAD: ic50=1.9uM
PDBbind-CN: -logKd/Ki=5.72,IC50=1.9uM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 N192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H41 D83 N173 G174 D175 S176 G177
Enzyme Commision number 3.4.21.117: stratum corneum chymotryptic enzyme.
Gene Ontology
Molecular Function
GO:0004222 metalloendopeptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0008233 peptidase activity
GO:0008236 serine-type peptidase activity
Biological Process
GO:0002803 positive regulation of antibacterial peptide production
GO:0006508 proteolysis
GO:0008544 epidermis development
GO:0022617 extracellular matrix disassembly
Cellular Component
GO:0001533 cornified envelope
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0030141 secretory granule
GO:0097209 epidermal lamellar body

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5y9l, PDBe:5y9l, PDBj:5y9l
PDBsum5y9l
PubMed29102227
UniProtP49862|KLK7_HUMAN Kallikrein-7 (Gene Name=KLK7)

[Back to BioLiP]