Structure of PDB 2zdm Chain A Binding Site BS02

Receptor Information
>2zdm 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 ID46U
InChIInChI=1S/C21H30N4O3/c22-20(23)16-10-8-15(9-11-16)13-24-21(27)18-7-4-12-25(18)19(26)14-28-17-5-2-1-3-6-17/h8-11,17-18H,1-7,12-14H2,(H3,22,23)(H,24,27)/t18-/m0/s1
InChIKeyIWPMQJKXKKKSEY-SFHVURJKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5c1cc(ccc1CNC(=O)C2CCCN2C(=O)COC3CCCCC3)C(=N)N
OpenEye OEToolkits 1.7.5[H]/N=C(/c1ccc(cc1)CNC(=O)[C@@H]2CCCN2C(=O)COC3CCCCC3)\N
CACTVS 3.385NC(=N)c1ccc(CNC(=O)[C@@H]2CCCN2C(=O)COC3CCCCC3)cc1
ACDLabs 12.01O=C(NCc1ccc(C(=[N@H])N)cc1)C3N(C(=O)COC2CCCCC2)CCC3
CACTVS 3.385NC(=N)c1ccc(CNC(=O)[CH]2CCCN2C(=O)COC3CCCCC3)cc1
FormulaC21 H30 N4 O3
Name(S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclohexyloxy)ethanoyl)pyrrolidine-2-carboxamide
ChEMBL
DrugBankDB07091
ZINCZINC000039019313
PDB chain2zdm Chain A Residue 501 [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]
PDB2zdm Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties
Resolution1.93 Å
Binding residue
(original residue number in PDB)		H57 T98 L99 D189 S190 C191 Q192 W215 G216 G219
Binding residue
(residue number reindexed from 1)		H40 T80 L81 D171 S172 C173 Q174 W193 G194 G196
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.41,Kd=386nM
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:2zdm, PDBe:2zdm, PDBj:2zdm
PDBsum2zdm
PubMed21111747
UniProtP00760|TRY1_BOVIN Serine protease 1 (Gene Name=PRSS1)

[Back to BioLiP]