Structure of PDB 2c8x Chain B

Receptor sequence

>2c8xB (length=251) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEGQPS
VLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGP
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
E

3D structure

• PDB: 2c8x Application of Fragment Screening and Fragment Linking to the Discovery of Novel Thrombin Inhibitors
• Chain: B
• Resolution: 2.17 Å

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.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	peptide	B	D21 E23 G25 M26 P28 W29 D116 H119 P120 C122 Y134 K135 R137 N159 M201 K202 N205 R206 W207	D6 E8 G10 M11 P13 W14 D113 H116 P117 C119 Y134 K135 R137 N156 M203 K204 N209 R210 W211
BS02	peptide	B	F34 Q38 L40 L65 R67 R73 T74 R75 Y76 K81 I82	F19 Q24 L26 L60 R62 R68 T69 R70 Y71 K77 I78
BS03	C5M	B	H57 Y60A W60D L99 D189 A190 S195 V213 W215 G216 G226 F227	H43 Y47 W50 L96 D191 A192 S197 V217 W219 G220 G230 F231	MOAD: ic50=220nM PDBbind-CN: -logKd/Ki=6.66,IC50=220nM BindingDB: IC50=220nM

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:2c8x, PDBe:2c8x, PDBj:2c8x
• PDBsum: 2c8x
• PubMed: 16480269
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)