Structure of PDB 3h8b Chain A Binding Site BS01

Receptor Information
>3h8b 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 IDNSY
InChIInChI=1S/C57H64N8O5/c58-57(59)62-36-15-25-50(56(70)65-51(38-42-18-7-2-8-19-42)54(68)61-37-34-41-16-5-1-6-17-41)64-55(69)49(63-53(67)40-44-28-32-48(33-29-44)46-22-11-4-12-23-46)24-13-14-35-60-52(66)39-43-26-30-47(31-27-43)45-20-9-3-10-21-45/h1-12,16-23,26-33,49-51H,13-15,24-25,34-40H2,(H,60,66)(H,61,68)(H,63,67)(H,64,69)(H,65,70)(H4,58,59,62)/t49-,50+,51-/m0/s1
InChIKeyYLNSEFZQVOPLSQ-HLRAQNEOSA-N
SMILES
SoftwareSMILES
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](Cc5ccccc5)C(=O)NCCc6ccccc6
OpenEye OEToolkits 1.7.0[H]/N=C(\N)/NCCC[C@H](C(=O)N[C@@H](Cc1ccccc1)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](Cc5ccccc5)C(=O)NCCc6ccccc6
OpenEye OEToolkits 1.7.0c1ccc(cc1)CCNC(=O)C(Cc2ccccc2)NC(=O)C(CCCNC(=N)N)NC(=O)C(CCCCNC(=O)Cc3ccc(cc3)c4ccccc4)NC(=O)Cc5ccc(cc5)c6ccccc6
ACDLabs 11.02O=C(NCCCCC(NC(=O)Cc2ccc(c1ccccc1)cc2)C(=O)NC(C(=O)NC(C(=O)NCCc3ccccc3)Cc4ccccc4)CCCNC(=[N@H])N)Cc6ccc(c5ccccc5)cc6
FormulaC57 H64 N8 O5
NameN~2~,N~6~-bis(biphenyl-4-ylacetyl)-L-lysyl-D-arginyl-N-(2-phenylethyl)-L-phenylalaninamide
ChEMBL
DrugBank
ZINCZINC000150344820
PDB chain3h8b 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3h8b A combined crystallographic and molecular dynamics study of cathepsin L retrobinding inhibitors
Resolution1.8 Å
Binding residue
(original residue number in PDB)		Q19 Q21 C22 G23 C25 G61 E63 G67 G68 L69 M70 A135 A138 G139 E141 L144 F145 D162 H163 W189
Binding residue
(residue number reindexed from 1)		Q19 Q21 C22 G23 C25 G61 E63 G67 G68 L69 M70 A135 A138 G139 E141 L144 F145 D162 H163 W184
Annotation score1
Binding affinityMOAD: Ki=0.511uM
PDBbind-CN: -logKd/Ki=6.29,Ki=0.511uM
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
View graph for
Biological Process
External links
PDB RCSB:3h8b, PDBe:3h8b, PDBj:3h8b
PDBsum3h8b
PubMed19761244
UniProtP07711|CATL1_HUMAN Procathepsin L (Gene Name=CTSL)

[Back to BioLiP]