Structure of PDB 3h89 Chain A Binding Site BS01

Receptor Information
>3h89 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 IDNSX
InChIInChI=1S/C57H64N8O6/c58-57(59)62-35-12-20-50(56(71)65-51(37-41-25-31-48(66)32-26-41)54(69)61-36-33-40-13-4-1-5-14-40)64-55(70)49(63-53(68)39-43-23-29-47(30-24-43)45-17-8-3-9-18-45)19-10-11-34-60-52(67)38-42-21-27-46(28-22-42)44-15-6-2-7-16-44/h1-9,13-18,21-32,49-51,66H,10-12,19-20,33-39H2,(H,60,67)(H,61,69)(H,63,68)(H,64,70)(H,65,71)(H4,58,59,62)/t49-,50+,51-/m0/s1
InChIKeyIFVMSTPAHOWZAK-HLRAQNEOSA-N
SMILES
SoftwareSMILES
ACDLabs 11.02O=C(NCCCCC(NC(=O)Cc2ccc(c1ccccc1)cc2)C(=O)NC(C(=O)NC(C(=O)NCCc3ccccc3)Cc4ccc(O)cc4)CCCNC(=[N@H])N)Cc6ccc(c5ccccc5)cc6
CACTVS 3.352NC(=N)NCCC[C@@H](NC(=O)[C@H](CCCCNC(=O)Cc1ccc(cc1)c2ccccc2)NC(=O)Cc3ccc(cc3)c4ccccc4)C(=O)N[C@@H](Cc5ccc(O)cc5)C(=O)NCCc6ccccc6
OpenEye OEToolkits 1.7.0c1ccc(cc1)CCNC(=O)C(Cc2ccc(cc2)O)NC(=O)C(CCCNC(=N)N)NC(=O)C(CCCCNC(=O)Cc3ccc(cc3)c4ccccc4)NC(=O)Cc5ccc(cc5)c6ccccc6
OpenEye OEToolkits 1.7.0[H]/N=C(\N)/NCCC[C@H](C(=O)N[C@@H](Cc1ccc(cc1)O)C(=O)NCCc2ccccc2)NC(=O)[C@H](CCCCNC(=O)Cc3ccc(cc3)c4ccccc4)NC(=O)Cc5ccc(cc5)c6ccccc6
CACTVS 3.352NC(=N)NCCC[CH](NC(=O)[CH](CCCCNC(=O)Cc1ccc(cc1)c2ccccc2)NC(=O)Cc3ccc(cc3)c4ccccc4)C(=O)N[CH](Cc5ccc(O)cc5)C(=O)NCCc6ccccc6
FormulaC57 H64 N8 O6
NameN~2~,N~6~-bis(biphenyl-4-ylacetyl)-L-lysyl-D-arginyl-N-(2-phenylethyl)-L-tyrosinamide
ChEMBL
DrugBank
ZINCZINC000150344818
PDB chain3h89 Chain A Residue 400 [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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PDB3h89 A combined crystallographic and molecular dynamics study of cathepsin L retrobinding inhibitors
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Q19 C25 E63 G67 G68 L69 M70 A135 A138 G139 H140 E141 L144 F145 D162 H163 A214
Binding residue
(residue number reindexed from 1)		Q19 C25 E63 G67 G68 L69 M70 A135 A138 G139 H140 E141 L144 F145 D162 H163 A209
Annotation score1
Binding affinityMOAD: Ki=0.023uM
PDBbind-CN: -logKd/Ki=7.64,Ki=0.023uM
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:3h89, PDBe:3h89, PDBj:3h89
PDBsum3h89
PubMed19761244
UniProtP07711|CATL1_HUMAN Procathepsin L (Gene Name=CTSL)

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