Structure of PDB 5mm6 Chain H Binding Site BS03

Receptor Information
>5mm6 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
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDSCEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
G
Ligand information
Ligand ID32U
InChIInChI=1S/C22H27N5O2/c23-18(13-15-5-2-1-3-6-15)22(29)27-12-4-7-19(27)21(28)26-14-16-8-10-17(11-9-16)20(24)25/h1-3,5-6,8-11,18-19H,4,7,12-14,23H2,(H3,24,25)(H,26,28)/p+1/t18-,19+/m1/s1
InChIKeyVZFTWWJAUZOJDH-MOPGFXCFSA-O
SMILES
SoftwareSMILES
CACTVS 3.385N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3ccc(cc3)C(N)=[NH2+]
ACDLabs 12.01O=C(NCc1ccc(C(=[NH2+])\\N)cc1)C3N(C(=O)C(N)Cc2ccccc2)CCC3
CACTVS 3.385N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccc(cc3)C(N)=[NH2+]
OpenEye OEToolkits 1.7.5c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3ccc(cc3)C(=[NH2+])N)N
OpenEye OEToolkits 1.7.5c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3ccc(cc3)C(=[NH2+])N)N
FormulaC22 H28 N5 O2
NameD-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-L-prolinamide
ChEMBL
DrugBankDB07005
ZINC
PDB chain5mm6 Chain H Residue 311 [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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PDB5mm6 Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide
Resolution1.29 Å
Binding residue
(original residue number in PDB)		H57 Y60A N98 L99 I174 D189 S190 V213 W215 G216
Binding residue
(residue number reindexed from 1)		H43 Y47 N95 L96 I172 D192 S193 V218 W220 G221
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 E192 G193 D194 S195
Catalytic site (residue number reindexed from 1) H43 D99 E195 G196 D197 S198
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:5mm6, PDBe:5mm6, PDBj:5mm6
PDBsum5mm6
PubMed
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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