Structure of PDB 2c8y Chain B Binding Site BS01

Receptor Information

>2c8y Chain B (length=251) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEGQPS
VLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGP
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
E

Ligand information

>2c8y Chain A (length=29) Species: 9606 (Homo sapiens)

GEADCGLRPLFEKKSLEDKTERELLESYI

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2c8y Application of Fragment Screening and Fragment Linking to the Discovery of Novel Thrombin Inhibitors
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): E23 I24 G25 M26 P28 W29 D116 H119 P120 C122 Y134 K135 R137 N159 M201 K202 P204 N205 R206 W207
• Binding residue (residue number reindexed from 1): E8 I9 G10 M11 P13 W14 D113 H116 P117 C119 Y134 K135 R137 N156 M203 K204 P206 N209 R210 W211

Enzymatic activity

• Catalytic site (original residue number in PDB): H57 D102 E192 G193 D194 S195 G196
• 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

External links

• PDB: RCSB:2c8y, PDBe:2c8y, PDBj:2c8y
• PDBsum: 2c8y
• PubMed: 16480269
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)