Structure of PDB 1ypl Chain H Binding Site BS03

Receptor Information
>1ypl Chain H (length=250) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
Ligand information
Ligand IDRA8
InChIInChI=1S/C23H38N6O4S/c1-17(2)15-19(28-34(32,33)16-18-9-4-3-5-10-18)22(31)29-14-8-11-20(29)21(30)26-12-6-7-13-27-23(24)25/h3-5,9-10,17,19-20,28H,6-8,11-16H2,1-2H3,(H,26,30)(H4,24,25,27)/t19-,20-/m0/s1
InChIKeyDSVCYWOHJLRGMK-PMACEKPBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)C[CH](N[S](=O)(=O)Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCCCCNC(N)=N
OpenEye OEToolkits 1.7.5CC(C)CC(C(=O)N1CCCC1C(=O)NCCCCNC(=N)N)NS(=O)(=O)Cc2ccccc2
ACDLabs 12.01O=C(NCCCCNC(=[N@H])N)C2N(C(=O)C(NS(=O)(=O)Cc1ccccc1)CC(C)C)CCC2
CACTVS 3.385CC(C)C[C@H](N[S](=O)(=O)Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCCCCNC(N)=N
OpenEye OEToolkits 1.7.5[H]/N=C(/N)\NCCCCNC(=O)[C@@H]1CCCN1C(=O)[C@H](CC(C)C)NS(=O)(=O)Cc2ccccc2
FormulaC23 H38 N6 O4 S
NameN-(BENZYLSULFONYL)-L-LEUCYL-N-(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)-L-PROLINAMIDE;
1-GUANIDINO-4-(N-PHENYLMETHANESULFONYL-L-LEUCYL-L-PROLYLAMINO)BUTANE
ChEMBL
DrugBankDB04772
ZINCZINC000016051709
PDB chain1ypl Chain H Residue 5555 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1ypl Design and X-ray crystal structures of human thrombin with synthetic cyanopeptide-analogues.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		H57 Y60A E97A L99 I174 D189 A190 S195 W215 G216
Binding residue
(residue number reindexed from 1)		H43 Y47 E94 L96 I172 D192 A193 S198 W220 G221
Annotation score1
Binding affinityMOAD: Ki=10.6uM
Enzymatic activity
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:1ypl, PDBe:1ypl, PDBj:1ypl
PDBsum1ypl
PubMed17341023
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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