Structure of PDB 3bc3 Chain A Binding Site BS01

Receptor Information
>3bc3 Chain A (length=215) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSE
QNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKY
NPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGI
YFEPDCSSEDMDHGVLVVGYGFESNKYWLVKNSWGEEWGMGGYVKMAKDR
RNHCGIASAASYPTV
Ligand information
Ligand IDOPT
InChIInChI=1S/C47H55N7O5S/c48-47(49)51-27-10-17-40(45(58)54-41(29-34-20-24-39(55)25-21-34)44(57)50-28-26-33-11-4-1-5-12-33)53-46(59)42(32-60-31-36-13-6-2-7-14-36)52-43(56)30-35-18-22-38(23-19-35)37-15-8-3-9-16-37/h1-9,11-16,18-25,40-42,47,51,55H,10,17,26-32,48-49H2,(H,50,57)(H,52,56)(H,53,59)(H,54,58)/t40-,41+,42+/m1/s1
InChIKeyIMZNRHOMBTZKJS-IWSHAHEXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc(cc1)CCNC(=O)[C@H](Cc2ccc(cc2)O)NC(=O)[C@@H](CCCNC(N)N)NC(=O)[C@H](CSCc3ccccc3)NC(=O)Cc4ccc(cc4)c5ccccc5
ACDLabs 10.04O=C(NC(C(=O)NC(C(=O)NC(C(=O)NCCc1ccccc1)Cc2ccc(O)cc2)CCCNC(N)N)CSCc3ccccc3)Cc5ccc(c4ccccc4)cc5
OpenEye OEToolkits 1.5.0c1ccc(cc1)CCNC(=O)C(Cc2ccc(cc2)O)NC(=O)C(CCCNC(N)N)NC(=O)C(CSCc3ccccc3)NC(=O)Cc4ccc(cc4)c5ccccc5
CACTVS 3.341NC(N)NCCC[C@@H](NC(=O)[C@H](CSCc1ccccc1)NC(=O)Cc2ccc(cc2)c3ccccc3)C(=O)N[C@@H](Cc4ccc(O)cc4)C(=O)NCCc5ccccc5
CACTVS 3.341NC(N)NCCC[CH](NC(=O)[CH](CSCc1ccccc1)NC(=O)Cc2ccc(cc2)c3ccccc3)C(=O)N[CH](Cc4ccc(O)cc4)C(=O)NCCc5ccccc5
FormulaC47 H55 N7 O5 S
NameS-benzyl-N-(biphenyl-4-ylacetyl)-L-cysteinyl-N~5~-(diaminomethyl)-D-ornithyl-N-(2-phenylethyl)-L-tyrosinamide
ChEMBL
DrugBank
ZINCZINC000098209272
PDB chain3bc3 Chain A Residue 300 [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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PDB3bc3 Exploring inhibitor binding at the S' subsites of cathepsin L
Resolution2.2 Å
Binding residue
(original residue number in PDB)		Q19 A25 G61 E63 G67 G68 L69 M70 A135 L144 M161 D162 H163 W189 A214
Binding residue
(residue number reindexed from 1)		Q19 A25 G61 E63 G67 G68 L69 M70 A135 L144 M161 D162 H163 W184 A209
Annotation score1
Binding affinityMOAD: Ki=0.155uM
PDBbind-CN: -logKd/Ki=6.81,Ki=0.155uM
Enzymatic activity
Catalytic site (original residue number in PDB) Q19 C25 H163 N187
Catalytic site (residue number reindexed from 1) Q19 C25 H163 N182
Enzyme Commision number 3.4.22.15: cathepsin L.
Gene Ontology
Molecular Function
GO:0008234 cysteine-type peptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:3bc3, PDBe:3bc3, PDBj:3bc3
PDBsum3bc3
PubMed18278855
UniProtP07711|CATL1_HUMAN Procathepsin L (Gene Name=CTSL)

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