Structure of PDB 1k1m Chain A Binding Site BS02

Receptor Information
>1k1m 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 IDFD4
InChIInChI=1S/C26H29N5O4S/c1-18(32)30-11-13-31(14-12-30)26(33)24(16-19-5-4-8-22(15-19)25(27)28)29-36(34,35)23-10-9-20-6-2-3-7-21(20)17-23/h2-10,15,17,24,29H,11-14,16H2,1H3,(H3,27,28)/t24-/m0/s1
InChIKeyZUWBXGHMVKDMQO-DEOSSOPVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=O)N1CCN(CC1)C(=O)C(Cc2cccc(c2)C(=N)N)NS(=O)(=O)c3ccc4ccccc4c3
CACTVS 3.341CC(=O)N1CCN(CC1)C(=O)[CH](Cc2cccc(c2)C(N)=N)N[S](=O)(=O)c3ccc4ccccc4c3
ACDLabs 10.04O=C(N4CCN(C(=O)C(NS(=O)(=O)c2cc1ccccc1cc2)Cc3cc(C(=[N@H])N)ccc3)CC4)C
CACTVS 3.341CC(=O)N1CCN(CC1)C(=O)[C@H](Cc2cccc(c2)C(N)=N)N[S](=O)(=O)c3ccc4ccccc4c3
OpenEye OEToolkits 1.5.0CC(=O)N1CCN(CC1)C(=O)[C@H](Cc2cccc(c2)C(=N)N)NS(=O)(=O)c3ccc4ccccc4c3
FormulaC26 H29 N5 O4 S
NameN-ALPHA-(2-NAPHTHYLSULFONYL)-N(3-AMIDINO-L-PHENYLALANINYL)-4-ACETYL-PIPERAZINE
ChEMBLCHEMBL104815
DrugBankDB04125
ZINCZINC000012504152
PDB chain1k1m Chain A Residue 999 [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]
PDB1k1m Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		H57 L99 D189 S190 C191 Q192 W215 G216 G219
Binding residue
(residue number reindexed from 1)		H40 L81 D171 S172 C173 Q174 W193 G194 G196
Annotation score1
Binding affinityMOAD: Kd=40nM
PDBbind-CN: -logKd/Ki=7.40,Kd=40nM
BindingDB: Ki=99999999999999nM
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:1k1m, PDBe:1k1m, PDBj:1k1m
PDBsum1k1m
PubMed11676542
UniProtP00760|TRY1_BOVIN Serine protease 1 (Gene Name=PRSS1)

[Back to BioLiP]