Structure of PDB 1ypm Chain H Binding Site BS03

Receptor Information
>1ypm 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 IDRA4
InChIInChI=1S/C23H35N7O5/c1-15(2)14-18(28-20(31)16-7-9-17(10-8-16)30(34)35)22(33)29-13-5-6-19(29)21(32)26-11-3-4-12-27-23(24)25/h7-10,15,18-19H,3-6,11-14H2,1-2H3,(H,26,32)(H,28,31)(H4,24,25,27)/t18-,19-/m0/s1
InChIKeyFIZYZWLGMGGGBJ-OALUTQOASA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)C[C@H](NC(=O)c1ccc(cc1)[N+]([O-])=O)C(=O)N2CCC[C@H]2C(=O)NCCCCNC(N)=N
ACDLabs 12.01O=C(NCCCCNC(=[N@H])N)C2N(C(=O)C(NC(=O)c1ccc([N+]([O-])=O)cc1)CC(C)C)CCC2
OpenEye OEToolkits 1.7.5CC(C)CC(C(=O)N1CCCC1C(=O)NCCCCNC(=N)N)NC(=O)c2ccc(cc2)[N+](=O)[O-]
CACTVS 3.385CC(C)C[CH](NC(=O)c1ccc(cc1)[N+]([O-])=O)C(=O)N2CCC[CH]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)NC(=O)c2ccc(cc2)[N+](=O)[O-]
FormulaC23 H35 N7 O5
NameN-(4-NITROBENZOYL)-L-LEUCYL-N-(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)-L-PROLINAMIDE;
1-GUANIDINO-4-(N-NITRO-BENZOYLAMINO-L-LEUCYL-L-PROLYLAMINO)BUTANE
ChEMBL
DrugBankDB04771
ZINCZINC000016051710
PDB chain1ypm 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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PDB1ypm 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 W60D N98 D189 A190 S195 S214 W215 G216 E217 G219 R221A
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 N95 D192 A193 S198 S219 W220 G221 E222 G223 R226
Annotation score1
Binding affinityMOAD: Ki=1.9uM
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:1ypm, PDBe:1ypm, PDBj:1ypm
PDBsum1ypm
PubMed17341023
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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