Structure of PDB 1c1u Chain H Binding Site BS03

Receptor Information
>1c1u 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
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
GE
Ligand information
Ligand IDBAI
InChIInChI=1S/C16H14N6/c17-16(18)9-5-6-12-13(7-9)22-15(21-12)8-14-19-10-3-1-2-4-11(10)20-14/h1-7H,8H2,(H3,17,18)(H,19,20)(H,21,22)
InChIKeyKKJYVDXDZURHMA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04[N@H]=C(c4ccc1c(nc(n1)Cc2nc3ccccc3n2)c4)N
CACTVS 3.341NC(=N)c1ccc2[nH]c(Cc3[nH]c4ccccc4n3)nc2c1
OpenEye OEToolkits 1.5.0c1ccc2c(c1)[nH]c(n2)Cc3[nH]c4ccc(cc4n3)C(=N)N
FormulaC16 H14 N6
Name(5-AMIDINO-2-BENZIMIDAZOLYL)(2-BENZIMIDAZOLYL)METHANE;
HEMI-BABIM
ChEMBLCHEMBL46148
DrugBankDB01767
ZINCZINC000002047318
PDB chain1c1u Chain H Residue 410 [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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PDB1c1u Design of potent selective zinc-mediated serine protease inhibitors.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		K60F D195 A196 E198 S201 G222
Binding residue
(residue number reindexed from 1)		K52 D192 A193 E195 S198 G221
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.25,Ki=0.0056uM
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
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Biological Process
External links
PDB RCSB:1c1u, PDBe:1c1u, PDBj:1c1u
PDBsum1c1u
PubMed9468142
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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