Structure of PDB 1ypg Chain H Binding Site BS03

Receptor Information
>1ypg Chain H (length=251) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETKGQ
PSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSG
GPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQ
F
Ligand information
Ligand IDUIR
InChIInChI=1S/C27H30N4O3/c28-26(29)18-8-6-17(7-9-18)25-23-22(19-2-1-11-30(19)25)24(16-4-5-16)31(27(23)32)13-15-3-10-20-21(12-15)34-14-33-20/h3,6-10,12,16,19,22-25H,1-2,4-5,11,13-14H2,(H3,28,29)/t19-,22-,23-,24+,25-/m0/s1
InChIKeyXYMBMAVAMICSMV-FTSNLURZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(ccc1[C@H]2[C@@H]3[C@H]([C@H]4[N@@]2CCC4)[C@H](N(C3=O)Cc5ccc6c(c5)OCO6)C7CC7)C(=N)N
OpenEye OEToolkits 1.5.0c1cc(ccc1C2C3C(C4N2CCC4)C(N(C3=O)Cc5ccc6c(c5)OCO6)C7CC7)C(=N)N
ACDLabs 10.04O=C2N(C(C1CC1)C5C2C(c3ccc(C(=[N@H])N)cc3)N4CCCC45)Cc6ccc7OCOc7c6
CACTVS 3.341NC(=N)c1ccc(cc1)[CH]2[CH]3[CH]([CH]4CCCN24)[CH](C5CC5)N(Cc6ccc7OCOc7c6)C3=O
CACTVS 3.341NC(=N)c1ccc(cc1)[C@H]2[C@@H]3[C@H]([C@@H]4CCCN24)[C@@H](C5CC5)N(Cc6ccc7OCOc7c6)C3=O
FormulaC27 H30 N4 O3
Name(1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL-5-YL-1-CYCLOPROPYL-3-OXO-DECAHYDRO-PYRROLO[3,4-A]PYRROLIZIN-4-YL)-BENZAMIDINE
ChEMBL
DrugBank
ZINCZINC000003832149
PDB chain1ypg 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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PDB1ypg A simple protocol to estimate differences in protein binding affinity for enantiomers without prior resolution of racemates
Resolution1.8 Å
Binding residue
(original residue number in PDB)		H57 Y60A E97A N98 D189 A190 W215 G216 G219
Binding residue
(residue number reindexed from 1)		H43 Y47 E94 N95 D193 A194 W221 G222 G224
Annotation score1
Binding affinityMOAD: Ki=10nM
PDBbind-CN: -logKd/Ki=8.00,Ki=10nM
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:1ypg, PDBe:1ypg, PDBj:1ypg
PDBsum1ypg
PubMed16374786
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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