Structure of PDB 2bdl Chain A Binding Site BS01

Receptor Information
>2bdl 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]
APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSP
QNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNP
TGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVY
YDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNK
NNACGIANLASFPKM
Ligand information
Ligand ID4PR
InChIInChI=1S/C28H41N5O6/c1-7-8-14-21(24(34)25(35)29-17(2)20-12-10-9-11-13-20)30-27(37)38-22-15-33(16-28(22,5)6)26(36)31-23-18(3)32-39-19(23)4/h9-13,17,21-22,24,34H,7-8,14-16H2,1-6H3,(H,29,35)(H,30,37)(H,31,36)/t17-,21+,22-,24+/m1/s1
InChIKeyVVZICJQTDYOKIN-TYVKFHQSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCC(C(C(=O)NC(C)c1ccccc1)O)NC(=O)OC2CN(CC2(C)C)C(=O)Nc3c(noc3C)C
CACTVS 3.341CCCC[CH](NC(=O)O[CH]1CN(CC1(C)C)C(=O)Nc2c(C)onc2C)[CH](O)C(=O)N[CH](C)c3ccccc3
OpenEye OEToolkits 1.5.0CCCC[C@@H]([C@@H](C(=O)N[C@H](C)c1ccccc1)O)NC(=O)O[C@@H]2CN(CC2(C)C)C(=O)Nc3c(noc3C)C
CACTVS 3.341CCCC[C@H](NC(=O)O[C@@H]1CN(CC1(C)C)C(=O)Nc2c(C)onc2C)[C@H](O)C(=O)N[C@H](C)c3ccccc3
ACDLabs 10.04O=C(Nc1c(onc1C)C)N3CC(C)(C)C(OC(=O)NC(C(O)C(=O)NC(c2ccccc2)C)CCCC)C3
FormulaC28 H41 N5 O6
Name(3S)-1-{[(3,5-DIMETHYLISOXAZOL-4-YL)AMINO]CARBONYL}-4,4-DIMETHYLPYRROLIDIN-3-YL{(1S)-1-[1-HYDROXY-2-OXO-2-{[(1R)-1-PHENYLETHYL]AMINO}ETHYL]PENTYL}CARBAMATE
ChEMBL
DrugBank
ZINCZINC000016051813
PDB chain2bdl Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2bdl Novel, potent P2-P3 pyrrolidine derivatives of ketoamide-based cathepsin K inhibitors.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		Q19 C22 G23 C25 G64 G65 G66 Y67 N161 H162 W184
Binding residue
(residue number reindexed from 1)		Q19 C22 G23 C25 G64 G65 G66 Y67 N161 H162 W184
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.82,IC50=15nM
Enzymatic activity
Catalytic site (original residue number in PDB) Q19 C25 H162 N182
Catalytic site (residue number reindexed from 1) Q19 C25 H162 N182
Enzyme Commision number 3.4.22.38: cathepsin K.
Gene Ontology
Molecular Function
GO:0008234 cysteine-type peptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:2bdl, PDBe:2bdl, PDBj:2bdl
PDBsum2bdl
PubMed16376075
UniProtP43235|CATK_HUMAN Cathepsin K (Gene Name=CTSK)

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