Structure of PDB 2pre Chain A Binding Site BS01

Receptor Information
>2pre Chain A (length=208) Species: 52861 (Tabernaemontana divaricata) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPEQIDWRKKGAVTPVKNQGKCGSCWAFSTVSTVESINQIRTGNLISLSE
QQLVDCNKKNHGCKGGAFVYAYQYIIDNGGIDTEANYPYKAVQGPCRAAK
KVVRIDGYKGVPHCNENALKKAVASQPSVVAIDASSKQFQHYKSGIFSGP
CGTKLNHGVVIVGYWKDYWIVRNSWGRYWGEQGYIRMKRVGGCGLCGIAR
LPYYPTKA
Ligand information
Ligand IDE64
InChIInChI=1S/C15H29N5O5/c1-9(2)7-10(20-14(25)11(21)8-12(22)23)13(24)18-5-3-4-6-19-15(16)17/h9-11,21H,3-8H2,1-2H3,(H,18,24)(H,20,25)(H,22,23)(H4,16,17,19)/p+1/t10-,11-/m0/s1
InChIKeyQPQNJAXBPHVASB-QWRGUYRKSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)C[C@@H](C(=O)NCCCCNC(=[NH2+])N)NC(=O)[C@H](CC(=O)O)O
OpenEye OEToolkits 1.5.0CC(C)CC(C(=O)NCCCCNC(=[NH2+])N)NC(=O)C(CC(=O)O)O
CACTVS 3.341CC(C)C[C@H](NC(=O)[C@@H](O)CC(O)=O)C(=O)NCCCCNC(N)=[NH2+]
CACTVS 3.341CC(C)C[CH](NC(=O)[CH](O)CC(O)=O)C(=O)NCCCCNC(N)=[NH2+]
ACDLabs 10.04O=C(O)CC(O)C(=O)NC(C(=O)NCCCCNC(=[NH2+])\N)CC(C)C
FormulaC15 H30 N5 O5
NameN-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
ChEMBL
DrugBankDB04276
ZINC
PDB chain2pre 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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PDB2pre Structural insights into the substrate specificity and activity of ervatamins, the papain-like cysteine proteases from a tropical plant, Ervatamia coronaria.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		Q19 G23 C25 H61 G65 N156 H157
Binding residue
(residue number reindexed from 1)		Q19 G23 C25 H61 G65 N156 H157
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.65,IC50=225nM
Enzymatic activity
Catalytic site (original residue number in PDB) Q19 C25 H157 N173
Catalytic site (residue number reindexed from 1) Q19 C25 H157 N173
Enzyme Commision number 3.4.22.-
Gene Ontology
Molecular Function
GO:0008234 cysteine-type peptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2pre, PDBe:2pre, PDBj:2pre
PDBsum2pre
PubMed18167146
UniProtA8DS38|ERVC2_TABDI Ervatamin-C

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