Structure of PDB 3gy3 Chain A Binding Site BS02

Receptor Information
>3gy3 Chain A (length=223) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRL
GEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRV
ASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKS
AYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQK
NKPGVYTKVCNYVSWIKQTIASN
Ligand information
Ligand IDPNT
InChIInChI=1S/C19H24N4O2/c20-18(21)14-4-8-16(9-5-14)24-12-2-1-3-13-25-17-10-6-15(7-11-17)19(22)23/h4-11H,1-3,12-13H2,(H3,20,21)(H3,22,23)
InChIKeyXDRYMKDFEDOLFX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O(c1ccc(cc1)C(=[N@H])N)CCCCCOc2ccc(C(=[N@H])N)cc2
CACTVS 3.341NC(=N)c1ccc(OCCCCCOc2ccc(cc2)C(N)=N)cc1
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=N)N)OCCCCCOc2ccc(cc2)C(=N)N
FormulaC19 H24 N4 O2
Name1,5-BIS(4-AMIDINOPHENOXY)PENTANE
ChEMBLCHEMBL55
DrugBankDB00738
ZINCZINC000001530775
PDB chain3gy3 Chain A Residue 246 [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]
PDB3gy3 Structural binding evidence of the trypanocidal drugs Berenil and Pentacarinate active principles to a serine protease model.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		H57 T98 L99 D189 S190 S214 W215 G216 G219
Binding residue
(residue number reindexed from 1)		H40 T80 L81 D171 S172 S192 W193 G194 G196
Annotation score1
Binding affinityMOAD: Kd=2.36uM
PDBbind-CN: -logKd/Ki=5.63,Kd=2.36uM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 Q192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H40 D84 Q174 G175 D176 S177 G178
Enzyme Commision number 3.4.21.4: trypsin.
Gene Ontology
Molecular Function
GO:0004175 endopeptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0005515 protein binding
GO:0008236 serine-type peptidase activity
GO:0046872 metal ion binding
GO:0097655 serpin family protein binding
Biological Process
GO:0006508 proteolysis
GO:0007586 digestion
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0097180 serine protease inhibitor complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3gy3, PDBe:3gy3, PDBj:3gy3
PDBsum3gy3
PubMed20356563
UniProtP00760|TRY1_BOVIN Serine protease 1 (Gene Name=PRSS1)

[Back to BioLiP]