Structure of PDB 1d3d Chain B Binding Site BS03

Receptor Information
>1d3d 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 IDBZT
InChIInChI=1S/C32H35BrN2O2S/c33-30-20-23(5-6-25(30)22-35-15-3-4-16-35)19-29-28-12-9-26(36)21-31(28)38-32(29)24-7-10-27(11-8-24)37-18-17-34-13-1-2-14-34/h5-12,20-21,36H,1-4,13-19,22H2
InChIKeyQVDZMCVSIVITGR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Oc1ccc2c(Cc3ccc(CN4CCCC4)c(Br)c3)c(sc2c1)c5ccc(OCCN6CCCC6)cc5
OpenEye OEToolkits 1.5.0c1cc(ccc1c2c(c3ccc(cc3s2)O)Cc4ccc(c(c4)Br)CN5CCCC5)OCCN6CCCC6
ACDLabs 10.04Brc1c(ccc(c1)Cc2c5ccc(O)cc5sc2c4ccc(OCCN3CCCC3)cc4)CN6CCCC6
FormulaC32 H35 Br N2 O2 S
Name3-(3-BROMO-4-PYRROLIDIN-1-YLMETHYL-BENZYL)-2-[4-PYRROLIDIN-1-YL-ETHOXY)-PHENYL]-BENZO[B]THIOPHEN-6-OL
ChEMBLCHEMBL275206
DrugBank
ZINCZINC000003834110
PDB chain1d3d 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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PDB1d3d 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
Resolution2.04 Å
Binding residue
(original residue number in PDB)		H79 Y83 W86 L132 D235 A236 C237 E238 V261 S262 W263 G264
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 L96 D192 A193 C194 E195 V218 S219 W220 G221
Annotation score1
Binding affinityMOAD: Ka=1240000000M^-1
PDBbind-CN: -logKd/Ki=9.09,Kd=0.81nM
BindingDB: Ki=2.1nM
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:1d3d, PDBe:1d3d, PDBj:1d3d
PDBsum1d3d
PubMed10739244
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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