Structure of PDB 5jfd Chain H Binding Site BS02

Receptor Information
>5jfd Chain H (length=252) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWGQ
PSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSG
GPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQ
FG
Ligand information
Ligand ID2TS
InChIInChI=1S/C26H36ClN7O4S/c27-21-11-10-19(15-28)20(14-21)16-32-24(35)23-9-5-13-34(23)25(36)22(8-4-12-31-26(29)30)33-39(37,38)17-18-6-2-1-3-7-18/h1-3,6-7,10-11,14,22-23,33H,4-5,8-9,12-13,15-17,28H2,(H,32,35)(H4,29,30,31)/t22-,23+/m1/s1
InChIKeyMWLLGEVAEDIFRC-PKTZIBPZSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NCc1cc(Cl)ccc1CN)C3N(C(=O)C(NS(=O)(=O)Cc2ccccc2)CCCNC(=[N@H])N)CCC3
CACTVS 3.385NCc1ccc(Cl)cc1CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](CCCNC(N)=N)N[S](=O)(=O)Cc3ccccc3
OpenEye OEToolkits 1.7.5[H]/N=C(\N)/NCCC[C@H](C(=O)N1CCC[C@H]1C(=O)NCc2cc(ccc2CN)Cl)NS(=O)(=O)Cc3ccccc3
CACTVS 3.385NCc1ccc(Cl)cc1CNC(=O)[CH]2CCCN2C(=O)[CH](CCCNC(N)=N)N[S](=O)(=O)Cc3ccccc3
OpenEye OEToolkits 1.7.5c1ccc(cc1)CS(=O)(=O)NC(CCCNC(=N)N)C(=O)N2CCCC2C(=O)NCc3cc(ccc3CN)Cl
FormulaC26 H36 Cl N7 O4 S
Name(2S)-N-[[2-(aminomethyl)-5-chloro-phenyl]methyl]-1-[(2R)-5-carbamimidamido-2-(phenylmethylsulfonylamino)pentanoyl]pyrrolidine-2-carboxamide;
(S)-1-((R)-5-Guanidino-2-phenylmethanesulfonylamino-pentanoyl)-pyrrolidine-2-carboxylic acid 2aminomethyl-5-chloro-benzylamide
ChEMBLCHEMBL1229260
DrugBank
ZINCZINC000039196557
PDB chain5jfd Chain H Residue 301 [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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PDB5jfd Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding.
Resolution1.46 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D I174 A190 S195 V213 S214 W215 G216 E217 G219 F227
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 I173 A194 S199 V219 S220 W221 G222 E223 G224 F233
Annotation score1
Binding affinityBindingDB: Ki=0.290000nM
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5jfd, PDBe:5jfd, PDBj:5jfd
PDBsum5jfd
PubMed31633354
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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