Structure of PDB 1tom Chain H Binding Site BS03

Receptor Information
>1tom 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
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEGQPS
VLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGP
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Ligand information
Ligand IDMIN
InChIInChI=1S/C22H34N4O2/c1-24-19(14-16-6-3-2-4-7-16)22(28)26-13-5-8-20(26)21(27)25-15-17-9-11-18(23)12-10-17/h2-4,6-7,17-20,24H,5,8-15,23H2,1H3,(H,25,27)/t17-,18-,19-,20+/m1/s1
InChIKeyMDSVGJAUFNXYRR-WTGUMLROSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CN[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCC3CCC(CC3)N
ACDLabs 12.01O=C(NCC1CCC(N)CC1)C3N(C(=O)C(NC)Cc2ccccc2)CCC3
CACTVS 3.370CN[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NC[C@@H]3CC[C@@H](N)CC3
OpenEye OEToolkits 1.7.0CNC(Cc1ccccc1)C(=O)N2CCCC2C(=O)NCC3CCC(CC3)N
CACTVS 3.370CN[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NC[CH]3CC[CH](N)CC3
FormulaC22 H34 N4 O2
NameMETHYL-PHE-PRO-AMINO-CYCLOHEXYLGLYCINE
ChEMBLCHEMBL125181
DrugBankDB08187
ZINCZINC000100036469
PDB chain1tom Chain H Residue 1 [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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PDB1tom Synthesis, evaluation, and crystallographic analysis of L-371,912: A potent and selective active-site thrombin inhibitor.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		Y60A W60D N98 L99 I174 A190 C191 W215 G216 G219
Binding residue
(residue number reindexed from 1)		Y47 W50 N95 L96 I171 A192 C193 W219 G220 G222
Annotation score1
Binding affinityMOAD: Ki=5nM
PDBbind-CN: -logKd/Ki=8.30,Ki=5nM
BindingDB: Ki=5nM,IC50=6nM
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:1tom, PDBe:1tom, PDBj:1tom
PDBsum1tom
PubMed
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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