Structure of PDB 1bb0 Chain B Binding Site BS03

Receptor Information
>1bb0 Chain B (length=249) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKPQELLCGASLISDRWVLTAAHCLLYPPWD
KNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIA
LMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEGQPSV
LQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPF
VMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Ligand information
Ligand ID0IV
InChIInChI=1S/C23H34N6O5S/c24-23(25)29-11-4-8-18(13-29)12-19(15-30)26-21(31)14-28-10-5-9-20(22(28)32)27-35(33,34)16-17-6-2-1-3-7-17/h1-3,6-7,15,18-20,27H,4-5,8-14,16H2,(H3,24,25)(H,26,31)/t18-,19+,20+/m1/s1
InChIKeyDATYERRDSFNBDN-AABGKKOBSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC(=N)N1CCC[C@H](C[C@H](NC(=O)CN2CCC[C@H](N[S](=O)(=O)Cc3ccccc3)C2=O)C=O)C1
ACDLabs 12.01O=C(NC(C=O)CC1CCCN(C(=[N@H])N)C1)CN3C(=O)C(NS(=O)(=O)Cc2ccccc2)CCC3
OpenEye OEToolkits 1.7.0c1ccc(cc1)CS(=O)(=O)NC2CCCN(C2=O)CC(=O)NC(CC3CCCN(C3)C(=N)N)C=O
OpenEye OEToolkits 1.7.0[H]/N=C(\N)/N1CCC[C@@H](C1)C[C@@H](C=O)NC(=O)CN2CCC[C@@H](C2=O)NS(=O)(=O)Cc3ccccc3
CACTVS 3.370NC(=N)N1CCC[CH](C[CH](NC(=O)CN2CCC[CH](N[S](=O)(=O)Cc3ccccc3)C2=O)C=O)C1
FormulaC23 H34 N6 O5 S
Name2-{(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}-N-{(2S)-1-[(3R)-1-carbamimidoylpiperidin-3-yl]-3-oxopropan-2-yl}acetamide;
CVS1694
ChEMBLCHEMBL342604
DrugBank
ZINCZINC000013760081
PDB chain1bb0 Chain B Residue 1 [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]
PDB1bb0 Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D I174 D189 C191 S195 S214 W215 G216 G219
Binding residue
(residue number reindexed from 1)		H42 Y46 W49 I170 D190 C192 S196 S217 W218 G219 G221
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.36,Ki=4.4nM
BindingDB: IC50=28.8nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 E192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H42 D98 E193 G194 D195 S196 G197
Enzyme Commision number 3.4.21.5: thrombin.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005509 calcium ion binding
Biological Process
GO:0006508 proteolysis
GO:0007596 blood coagulation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1bb0, PDBe:1bb0, PDBj:1bb0
PDBsum1bb0
PubMed9724521
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

[Back to BioLiP]