Structure of PDB 6zug Chain H Binding Site BS03

Receptor Information
>6zug 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 IDQPW
InChIInChI=1S/C24H28ClN3O4/c1-3-8-28(14-17-7-9-31-15-17)23(29)18-11-20-22(21(12-18)30-2)32-24(27-20)26-13-16-5-4-6-19(25)10-16/h4-6,10-12,17H,3,7-9,13-15H2,1-2H3,(H,26,27)/t17-/m0/s1
InChIKeyRYXSWCUDMULFML-KRWDZBQOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCN(C[CH]1CCOC1)C(=O)c2cc(OC)c3oc(NCc4cccc(Cl)c4)nc3c2
OpenEye OEToolkits 2.0.7CCCN(CC1CCOC1)C(=O)c2cc3c(c(c2)OC)oc(n3)NCc4cccc(c4)Cl
OpenEye OEToolkits 2.0.7CCCN(C[C@@H]1CCOC1)C(=O)c2cc3c(c(c2)OC)oc(n3)NCc4cccc(c4)Cl
CACTVS 3.385CCCN(C[C@@H]1CCOC1)C(=O)c2cc(OC)c3oc(NCc4cccc(Cl)c4)nc3c2
FormulaC24 H28 Cl N3 O4
Name2-[(3-chlorophenyl)methylamino]-7-methoxy-~{N}-[[(3~{S})-oxolan-3-yl]methyl]-~{N}-propyl-1,3-benzoxazole-5-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6zug Chain H Residue 1001 [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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PDB6zug Design, Synthesis, and Pharmacological Characterization of a Neutral, Non-Prodrug Thrombin Inhibitor with Good Oral Pharmacokinetics.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D N98 L99 I174 D189 A190 C191 S195 V213 S214 W215 G216 E217 G219 G226 F227
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 N95 L96 I172 D192 A193 C194 S198 V218 S219 W220 G221 E222 G223 G231 F232
Annotation score1
Binding affinityMOAD: ic50=12nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 E192 G193 D194 S195 G196
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:6zug, PDBe:6zug, PDBj:6zug
PDBsum6zug
PubMed33108181
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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