Structure of PDB 6pad Chain A Binding Site BS01

Receptor Information

>6pad Chain A (length=212) Species: 3649 (Carica papaya)

IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSE
QELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREK
GPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFV
GPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVC
GLYTSSFYPVKN

Ligand information

• Ligand ID: 0PC
• InChI: InChI=1S/C21H23ClN2O4/c1-15(19(25)13-22)23-20(26)18(12-16-8-4-2-5-9-16)24-21(27)28-14-17-10-6-3-7-11-17/h2-11,15,18H,12-14H2,1H3,(H,23,26)(H,24,27)/t15-,18-/m0/s1
• InChIKey: YAWCSFNDFRSZKD-YJBOKZPZSA-N
• SMILES:
  CACTVS 3.370: C[CH](NC(=O)[CH](Cc1ccccc1)NC(=O)OCc2ccccc2)C(=O)CCl
  OpenEye OEToolkits 1.7.0: CC(C(=O)CCl)NC(=O)C(Cc1ccccc1)NC(=O)OCc2ccccc2
  CACTVS 3.370: C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)OCc2ccccc2)C(=O)CCl
  ACDLabs 12.01: ClCC(=O)C(NC(=O)C(NC(=O)OCc1ccccc1)Cc2ccccc2)C
  OpenEye OEToolkits 1.7.0: C[C@@H](C(=O)CCl)NC(=O)[C@H](Cc1ccccc1)NC(=O)OCc2ccccc2
• Formula: C21 H23 Cl N2 O4
• Name: Nalpha-[(benzyloxy)carbonyl]-N-[(1S)-3-chloro-1-methyl-2-oxopropyl]-L-phenylalaninamide;
  ZPACK
• ChEMBL: CHEMBL2402202
• PDB chain: 6pad Chain A Residue 213

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6pad Binding of chloromethyl ketone substrate analogues to crystalline papain.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): G23 C25 Y61 G65 G66 Y67 V157 D158 H159
• Binding residue (residue number reindexed from 1): G23 C25 Y61 G65 G66 Y67 V157 D158 H159
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): V16 Q19 C25 N155 H159 N175
• Catalytic site (residue number reindexed from 1): V16 Q19 C25 N155 H159 N175
• Enzyme Commision number: 3.4.22.2: papain.

Gene Ontology

Molecular Function

• GO:0008234 cysteine-type peptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:6pad, PDBe:6pad, PDBj:6pad
• PDBsum: 6pad
• PubMed: 952885
• UniProt: P00784|PAPA1_CARPA Papain