Structure of PDB 6eo9 Chain H Binding Site BS03

Receptor Information
>6eo9 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 ID2OJ
InChIInChI=1S/C40H50ClN3O14S/c1-22(2)44-15-13-27(14-16-44)39(49)42-35-29(9-7-10-30(35)53-20-28-19-31(58-43-28)33-11-12-34(41)59-33)50-17-8-18-51-40-38(56-26(6)48)37(55-25(5)47)36(54-24(4)46)32(57-40)21-52-23(3)45/h7,9-12,19,22,27,32,36-38,40H,8,13-18,20-21H2,1-6H3,(H,42,49)/t32-,36-,37+,38-,40-/m1/s1
InChIKeyGNVQZTIXGHEXLF-NIURAOKHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)N1CCC(CC1)C(=O)Nc2c(OCCCO[C@@H]3O[C@H](COC(C)=O)[C@@H](OC(C)=O)[C@H](OC(C)=O)[C@H]3OC(C)=O)cccc2OCc4cc(on4)c5sc(Cl)cc5
ACDLabs 12.01Clc5sc(c1onc(c1)COc4cccc(OCCCOC2OC(COC(=O)C)C(OC(=O)C)C(OC(=O)C)C2OC(=O)C)c4NC(=O)C3CCN(C(C)C)CC3)cc5
OpenEye OEToolkits 1.7.6CC(C)N1CCC(CC1)C(=O)Nc2c(cccc2OCc3cc(on3)c4ccc(s4)Cl)OCCCOC5C(C(C(C(O5)COC(=O)C)OC(=O)C)OC(=O)C)OC(=O)C
CACTVS 3.385CC(C)N1CCC(CC1)C(=O)Nc2c(OCCCO[CH]3O[CH](COC(C)=O)[CH](OC(C)=O)[CH](OC(C)=O)[CH]3OC(C)=O)cccc2OCc4cc(on4)c5sc(Cl)cc5
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)COC(=O)C)OC(=O)C)OC(=O)C)OC(=O)C
FormulaC40 H50 Cl N3 O14 S
NameN-(2-{[5-(5-chlorothiophen-2-yl)-1,2-oxazol-3-yl]methoxy}-6-{3-[(2,3,4,6-tetra-O-acetyl-beta-D-glucopyranosyl)oxy]propoxy}phenyl)-1-(propan-2-yl)piperidine-4-carboxamide
ChEMBLCHEMBL3343300
DrugBank
ZINCZINC000150340312
PDB chain6eo9 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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PDB6eo9 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.
Resolution1.84 Å
Binding residue
(original residue number in PDB)		E97A I174 A190 V213 W215 G216 E217 G219 G226 F227 Y228
Binding residue
(residue number reindexed from 1)		E94 I172 A193 V218 W220 G221 E222 G223 G231 F232 Y233
Annotation score1
Binding affinityMOAD: Ki=160nM
PDBbind-CN: -logKd/Ki=6.80,Ki=160nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:6eo9, PDBe:6eo9, PDBj:6eo9
PDBsum6eo9
PubMed25268757
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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