Structure of PDB 1d3t Chain B Binding Site BS03

Receptor Information
>1d3t Chain B (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 IDBT1
InChIInChI=1S/C32H35N3O3S/c36-31(25-11-14-29(33-23-25)38-22-20-35-17-5-6-18-35)30-27-7-1-2-8-28(27)39-32(30)24-9-12-26(13-10-24)37-21-19-34-15-3-4-16-34/h1-2,7-14,23H,3-6,15-22H2
InChIKeyZWXFJUPNUWRODU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(c1c4ccccc4sc1c3ccc(OCCN2CCCC2)cc3)c6ccc(OCCN5CCCC5)nc6
CACTVS 3.341O=C(c1ccc(OCCN2CCCC2)nc1)c3c(sc4ccccc34)c5ccc(OCCN6CCCC6)cc5
OpenEye OEToolkits 1.5.0c1ccc2c(c1)c(c(s2)c3ccc(cc3)OCCN4CCCC4)C(=O)c5ccc(nc5)OCCN6CCCC6
FormulaC32 H35 N3 O3 S
Name{2-[4-(2-PYRROLIDIN-1-YL-ETHOXY)-PHENYL]-BENZO[B]THIOPHEN-3-YL}-[4-(2-PYRROLIDIN-1-YL-ETHOXY)-PHENYL]-METHANONE
ChEMBLCHEMBL82285
DrugBank
ZINCZINC000003875331
PDB chain1d3t Chain B Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1d3t The crystal structures of human alpha-thrombin complexed with active site-directed diamino benzo[b]thiophene derivatives: a binding mode for a structurally novel class of inhibitors.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		Y83 W86 E130 N131 D235 A236 C237 E238 W263 G264 G266 C267
Binding residue
(residue number reindexed from 1)		Y47 W50 E94 N95 D192 A193 C194 E195 W220 G221 G223 C224
Annotation score1
Binding affinityBindingDB: Ki=374nM
Enzymatic activity
Catalytic site (original residue number in PDB) H79 D135 E238 G239 D240 S241 G242
Catalytic site (residue number reindexed from 1) H43 D99 E195 G196 D197 S198 G199
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:1d3t, PDBe:1d3t, PDBj:1d3t
PDBsum1d3t
PubMed10739244
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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