Structure of PDB 4od9 Chain B Binding Site BS01

Receptor Information
>4od9 Chain B (length=240) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GVKVERQVFGEATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQ
QKLVDQNIFSFYLSRDPDAQPGGELMLGGTDSKYYKGSLSYLNVTRKAYW
QVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRELQKAIGAVPL
IQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQAGKTLCLSGF
MGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAA
Ligand information
Ligand ID2RZ
InChIInChI=1S/C29H34N4O6/c1-36-23-12-10-20(15-25(23)38-3)17-27(34)33-29(30)32-22(14-19-8-6-5-7-9-19)28(35)31-18-21-11-13-24(37-2)26(16-21)39-4/h5-13,15-16,22H,14,17-18H2,1-4H3,(H,31,35)(H3,30,32,33,34)/t22-/m1/s1
InChIKeyIZIUZEPBXLRZLW-JOCHJYFZSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NC(=[N@H])NC(C(=O)NCc1cc(OC)c(OC)cc1)Cc2ccccc2)Cc3ccc(OC)c(OC)c3
OpenEye OEToolkits 1.7.6COc1ccc(cc1OC)CC(=O)NC(=N)NC(Cc2ccccc2)C(=O)NCc3ccc(c(c3)OC)OC
CACTVS 3.385COc1ccc(CNC(=O)[CH](Cc2ccccc2)NC(=N)NC(=O)Cc3ccc(OC)c(OC)c3)cc1OC
OpenEye OEToolkits 1.7.6[H]/N=C(\N[C@H](Cc1ccccc1)C(=O)NCc2ccc(c(c2)OC)OC)/NC(=O)Cc3ccc(c(c3)OC)OC
CACTVS 3.385COc1ccc(CNC(=O)[C@@H](Cc2ccccc2)NC(=N)NC(=O)Cc3ccc(OC)c(OC)c3)cc1OC
FormulaC29 H34 N4 O6
NameN-(3,4-dimethoxybenzyl)-Nalpha-{N-[(3,4-dimethoxyphenyl)acetyl]carbamimidoyl}-D-phenylalaninamide
ChEMBLCHEMBL3321925
DrugBank
ZINCZINC000098208253
PDB chain4od9 Chain A Residue 103 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4od9 Structure-based optimization of non-peptidic Cathepsin D inhibitors.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		F126 F131 I134 Y205 I229 D231 G233 T234 M309 I311
Binding residue
(residue number reindexed from 1)		F20 F25 I28 Y99 I123 D125 G127 T128 M203 I205
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.24,IC50=58nM
BindingDB: IC50=58nM
Enzymatic activity
Catalytic site (original residue number in PDB) D231 T234
Catalytic site (residue number reindexed from 1) D125 T128
Enzyme Commision number 3.4.23.5: cathepsin D.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:4od9, PDBe:4od9, PDBj:4od9
PDBsum4od9
PubMed25086681
UniProtP07339|CATD_HUMAN Cathepsin D (Gene Name=CTSD)

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