Structure of PDB 2r2m Chain B Binding Site BS03

Receptor Information
>2r2m Chain B (length=249) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEGQPS
VLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGP
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
Ligand information
Ligand IDI50
InChIInChI=1S/C19H21ClF3N5O2/c20-14-6-7-15(27-11-19(22,23)12-4-2-1-3-5-12)17(21)13(14)10-16(29)26-8-9-30-28-18(24)25/h1-7,27H,8-11H2,(H,26,29)(H4,24,25,28)
InChIKeyDZEJHPMTDNDECN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0[H]/N=C(/N)\NOCCNC(=O)Cc1c(ccc(c1F)NCC(c2ccccc2)(F)F)Cl
OpenEye OEToolkits 1.5.0[H]N=C(N)NOCCNC(=O)Cc1c(ccc(c1F)NCC(c2ccccc2)(F)F)Cl
CACTVS 3.341NC(=N)NOCCNC(=O)Cc1c(F)c(NCC(F)(F)c2ccccc2)ccc1Cl
ACDLabs 10.04Clc1ccc(c(F)c1CC(=O)NCCONC(=[N@H])N)NCC(F)(F)c2ccccc2
FormulaC19 H21 Cl F3 N5 O2
NameN-[2-({[amino(imino)methyl]amino}oxy)ethyl]-2-{6-chloro-3-[(2,2-difluoro-2-phenylethyl)amino]-2-fluorophenyl}acetamide
ChEMBLCHEMBL401842
DrugBankDB07946
ZINCZINC000034241908
PDB chain2r2m Chain B Residue 5000 [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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PDB2r2m 2-(2-Chloro-6-Fluorophenyl)Acetamides as Potent Thrombin Inhibitors
Resolution2.1 Å
Binding residue
(original residue number in PDB)		H79 Y83 W86 E130 D229 A230 C231 S235 S256 W257 G258
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 E94 D191 A192 C193 S197 S218 W219 G220
Annotation score1
Binding affinityMOAD: Ki=47.1nM
PDBbind-CN: -logKd/Ki=7.33,Ki=47.1nM
Enzymatic activity
Catalytic site (original residue number in PDB) H79 D135 E232 G233 D234 S235 G236
Catalytic site (residue number reindexed from 1) H43 D99 E194 G195 D196 S197 G198
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:2r2m, PDBe:2r2m, PDBj:2r2m
PDBsum2r2m
PubMed17889527
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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