Structure of PDB 6tdt Chain H Binding Site BS02

Receptor Information
>6tdt Chain H (length=251) 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
G
Ligand information
Ligand IDLXW
InChIInChI=1S/C26H28N4O2/c27-24(23(20-8-3-1-4-9-20)21-10-5-2-6-11-21)26(32)30-17-7-12-22(30)25(31)29-18-19-13-15-28-16-14-19/h1-6,8-11,13-16,22-24H,7,12,17-18,27H2,(H,29,31)/t22-,24+/m0/s1
InChIKeyDPXLHPWLQSWEQB-LADGPHEKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)C(c2ccccc2)C(C(=O)N3CCCC3C(=O)NCc4ccncc4)N
OpenEye OEToolkits 2.0.7c1ccc(cc1)C(c2ccccc2)[C@H](C(=O)N3CCC[C@H]3C(=O)NCc4ccncc4)N
CACTVS 3.385N[C@H](C(c1ccccc1)c2ccccc2)C(=O)N3CCC[C@H]3C(=O)NCc4ccncc4
CACTVS 3.385N[CH](C(c1ccccc1)c2ccccc2)C(=O)N3CCC[CH]3C(=O)NCc4ccncc4
FormulaC26 H28 N4 O2
Name(2~{S})-1-[(2~{R})-2-azanyl-3,3-diphenyl-propanoyl]-~{N}-(pyridin-4-ylmethyl)pyrrolidine-2-carboxamide
ChEMBLCHEMBL4594624
DrugBank
ZINC
PDB chain6tdt Chain H Residue 305 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6tdt Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?
Resolution1.53 Å
Binding residue
(original residue number in PDB)		Y60A W60D N98 L99 I174 A190 E192 S195 S214 W215 G216 G219
Binding residue
(residue number reindexed from 1)		Y47 W50 N95 L96 I172 A193 E195 S198 S219 W220 G221 G223
Annotation score1
Binding affinityMOAD: Ki=1213nM
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:6tdt, PDBe:6tdt, PDBj:6tdt
PDBsum6tdt
PubMed32011145
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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