Structure of PDB 2gdd Chain B Binding Site BS01

Receptor Information
>2gdd Chain B (length=243) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDV
KDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEP
VKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKV
PIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVC
KVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK
Ligand information
Ligand ID5AM
InChIInChI=1S/C31H42N6O5/c32-17-8-7-15-26(33-31(40)41-23-25-12-5-2-6-13-25)29(39)30-34-27(42-35-30)22-36-18-20-37(21-19-36)28(38)16-9-14-24-10-3-1-4-11-24/h1-6,10-13,26,29,39H,7-9,14-23,32H2,(H,33,40)/t26-,29-/m0/s1
InChIKeyLRPAFCFDXNPFAF-WNJJXGMVSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(N3CCN(Cc1nc(no1)C(O)C(NC(=O)OCc2ccccc2)CCCCN)CC3)CCCc4ccccc4
OpenEye OEToolkits 1.5.0c1ccc(cc1)CCCC(=O)N2CCN(CC2)Cc3nc(no3)C(C(CCCCN)NC(=O)OCc4ccccc4)O
OpenEye OEToolkits 1.5.0c1ccc(cc1)CCCC(=O)N2CCN(CC2)Cc3nc(no3)[C@H]([C@H](CCCCN)NC(=O)OCc4ccccc4)O
CACTVS 3.341NCCCC[C@H](NC(=O)OCc1ccccc1)[C@H](O)c2noc(CN3CCN(CC3)C(=O)CCCc4ccccc4)n2
CACTVS 3.341NCCCC[CH](NC(=O)OCc1ccccc1)[CH](O)c2noc(CN3CCN(CC3)C(=O)CCCc4ccccc4)n2
FormulaC31 H42 N6 O5
NameBENZYL {(1S)-5-AMINO-1-[(S)-HYDROXY(5-{[4-(4-PHENYLBUTANOYL)PIPERAZIN-1-YL]METHYL}-1,2,4-OXADIAZOL-3-YL)METHYL]PENTYL}CARBAMATE
ChEMBL
DrugBank
ZINCZINC000016052062
PDB chain2gdd Chain B Residue 998 [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]
PDB2gdd Human beta II tryptase with inhibitor CRA-27592
Resolution2.35 Å
Binding residue
(original residue number in PDB)		F41 H57 K60D L64 D189 S190 Q192 G193 S195 V213 S214 W215
Binding residue
(residue number reindexed from 1)		F28 H44 K51 L56 D188 S189 Q191 G192 S194 V212 S213 W214
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 Q192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H44 D91 Q191 G192 D193 S194 G195
Enzyme Commision number 3.4.21.59: tryptase.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005515 protein binding
GO:0008236 serine-type peptidase activity
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0062023 collagen-containing extracellular matrix

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2gdd, PDBe:2gdd, PDBj:2gdd
PDBsum2gdd
PubMed
UniProtP20231|TRYB2_HUMAN Tryptase beta-2 (Gene Name=TPSB2)

[Back to BioLiP]