Structure of PDB 5yjm Chain A Binding Site BS02

Receptor Information
>5yjm Chain A (length=218) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IIGGTESKPHSRPYMAYLEIVTSNGPSKFCGGFLIRRNFVLTAAHCAGRS
ITVTLGAHNITEEEDTWQKLEVIKQFRHPKYNTSTLHHDIMLLKLKEKAS
LTLAVGTLPFPGRMCRVAGWGRTGVLKPGSDTLQEVKLRLMDPQACSHFR
DFDHNLQLCVGNPRKTKSAFKGDSGGPLLCAGVAQGIVSYGRSDAKPPAV
FTRISHYRPWINQILQAN
Ligand information
Ligand ID8W3
InChIInChI=1S/C30H32ClN5O6/c1-3-25(18-9-11-23(29(38)39)24(32)15-18)34-30(40)36-17-27(35-42-22-7-5-4-6-8-22)33-16-20(28(36)37)13-19-14-21(31)10-12-26(19)41-2/h4-12,14-15,20,25H,3,13,16-17,32H2,1-2H3,(H,33,35)(H,34,40)(H,38,39)/t20-,25-/m1/s1
InChIKeyLHASZEBEQGPCFM-CJFMBICVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCC(c1ccc(c(c1)N)C(=O)O)NC(=O)N2CC(=NOc3ccccc3)NCC(C2=O)Cc4cc(ccc4OC)Cl
CACTVS 3.385CC[C@@H](NC(=O)N1CC(/NC[C@@H](Cc2cc(Cl)ccc2OC)C1=O)=N/Oc3ccccc3)c4ccc(C(O)=O)c(N)c4
CACTVS 3.385CC[CH](NC(=O)N1CC(NC[CH](Cc2cc(Cl)ccc2OC)C1=O)=NOc3ccccc3)c4ccc(C(O)=O)c(N)c4
OpenEye OEToolkits 2.0.6CC[C@H](c1ccc(c(c1)N)C(=O)O)NC(=O)N2C/C(=N/Oc3ccccc3)/NC[C@H](C2=O)Cc4cc(ccc4OC)Cl
FormulaC30 H32 Cl N5 O6
Name2-amino-4-((R)-1-((R,Z)-6-(5-chloro-2-methoxybenzyl)-7-oxo-3-(phenoxyimino)-1,4-diazepane-1-carboxamido)propyl)benzoic acid;
2-azanyl-4-[(1R)-1-[[(3Z,6R)-6-[(5-chloranyl-2-methoxy-phenyl)methyl]-7-oxidanylidene-3-phenoxyimino-1,4-diazepan-1-yl] carbonylamino]propyl]benzoic acid
ChEMBLCHEMBL4206099
DrugBank
ZINCZINC000169707613
PDB chain5yjm Chain A Residue 304 [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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PDB5yjm Structure-based design, synthesis, and binding mode analysis of novel and potent chymase inhibitors
Resolution1.9 Å
Binding residue
(original residue number in PDB)		F41 C42 H57 Y94 L99 D102 R143 A190 F191 K192 S195 S214 G216 R217
Binding residue
(residue number reindexed from 1)		F29 C30 H45 Y81 L86 D89 R122 A169 F170 K171 S174 S189 G191 R192
Annotation score1
Binding affinityMOAD: Kd=0.000000064M
PDBbind-CN: -logKd/Ki=7.68,Kd=21nM
BindingDB: Kd=2.1nM,IC50=8.9nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 K192 G193 D194 S195
Catalytic site (residue number reindexed from 1) H45 D89 K171 G172 D173 S174
Enzyme Commision number 3.4.21.39: chymase.
Gene Ontology
Molecular Function
GO:0004175 endopeptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0008236 serine-type peptidase activity
GO:0042277 peptide binding
Biological Process
GO:0002003 angiotensin maturation
GO:0006508 proteolysis
GO:0006518 peptide metabolic process
GO:0016485 protein processing
GO:0022617 extracellular matrix disassembly
GO:0030163 protein catabolic process
GO:0030901 midbrain development
GO:0034769 basement membrane disassembly
GO:0045766 positive regulation of angiogenesis
GO:0050727 regulation of inflammatory response
GO:0071333 cellular response to glucose stimulus
GO:0140447 cytokine precursor processing
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0030141 secretory granule
GO:0036464 cytoplasmic ribonucleoprotein granule
GO:0043231 intracellular membrane-bounded organelle
GO:0062023 collagen-containing extracellular matrix

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yjm, PDBe:5yjm, PDBj:5yjm
PDBsum5yjm
PubMed29191554
UniProtP23946|CMA1_HUMAN Chymase (Gene Name=CMA1)

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