Structure of PDB 6eo8 Chain H Binding Site BS03

Receptor Information
>6eo8 Chain H (length=247) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEQPSV
LQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPF
VMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQ
Ligand information
Ligand ID2FN
InChIInChI=1S/C32H42ClN3O10S/c1-18(2)36-11-9-19(10-12-36)31(41)34-27-21(42-13-4-14-43-32-30(40)29(39)28(38)24(16-37)45-32)5-3-6-22(27)44-17-20-15-23(46-35-20)25-7-8-26(33)47-25/h3,5-8,15,18-19,24,28-30,32,37-40H,4,9-14,16-17H2,1-2H3,(H,34,41)/t24-,28-,29+,30-,32-/m1/s1
InChIKeyOSTBNMJDSAVEFJ-JFJWUYLVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)N1CCC(CC1)C(=O)Nc2c(cccc2OCc3cc(on3)c4ccc(s4)Cl)OCCCO[C@H]5[C@@H]([C@H]([C@@H]([C@H](O5)CO)O)O)O
OpenEye OEToolkits 1.7.6CC(C)N1CCC(CC1)C(=O)Nc2c(cccc2OCc3cc(on3)c4ccc(s4)Cl)OCCCOC5C(C(C(C(O5)CO)O)O)O
CACTVS 3.385CC(C)N1CCC(CC1)C(=O)Nc2c(OCCCO[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)cccc2OCc4cc(on4)c5sc(Cl)cc5
ACDLabs 12.01Clc5sc(c1onc(c1)COc4cccc(OCCCOC2OC(CO)C(O)C(O)C2O)c4NC(=O)C3CCN(C(C)C)CC3)cc5
CACTVS 3.385CC(C)N1CCC(CC1)C(=O)Nc2c(OCCCO[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O)cccc2OCc4cc(on4)c5sc(Cl)cc5
FormulaC32 H42 Cl N3 O10 S
NameN-(2-{[5-(5-chlorothiophen-2-yl)-1,2-oxazol-3-yl]methoxy}-6-[3-(beta-D-glucopyranosyloxy)propoxy]phenyl)-1-(propan-2-yl)piperidine-4-carboxamide
ChEMBLCHEMBL3343301
DrugBank
ZINCZINC000098208159
PDB chain6eo8 Chain H Residue 307 [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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PDB6eo8 How a beta-D-glucoside side chain enhances binding affinity to thrombin of inhibitors bearing 2-chlorothiophene as P1 moiety: crystallography, fragment deconstruction study, and evaluation of antithrombotic properties.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		I174 D189 A190 V213 W215 G216 E217 G219 R221A G226 F227 Y228
Binding residue
(residue number reindexed from 1)		I170 D190 A191 V216 W218 G219 E220 G221 R224 G229 F230 Y231
Annotation score1
Binding affinityMOAD: Ki=100nM
PDBbind-CN: -logKd/Ki=7.00,Ki=100nM
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:6eo8, PDBe:6eo8, PDBj:6eo8
PDBsum6eo8
PubMed25268757
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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