Structure of PDB 2c8y Chain B

Receptor sequence

>2c8yB (length=251) Species: 9606 (Homo sapiens) [Search protein sequence]

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEGQPS
VLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGP
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
E

3D structure

PDB

2c8y Application of Fragment Screening and Fragment Linking to the Discovery of Novel Thrombin Inhibitors

Chain

Resolution

2.2 Å

3D
structure

Catalytic site residues are labeled in the structure
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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	E23 I24 G25 M26 P28 W29 D116 H119 P120 C122 Y134 K135 R137 N159 M201 K202 P204 N205 R206 W207	E8 I9 G10 M11 P13 W14 D113 H116 P117 C119 Y134 K135 R137 N156 M203 K204 P206 N209 R210 W211
BS02	peptide	B	F34 L65 R67 R73 T74 R75 Y76 K81 I82	F19 L60 R62 R68 T69 R70 Y71 K77 I78
BS03	C3M	B	H57 Y60A W60D N98 L99 W215 G216	H43 Y47 W50 N95 L96 W219 G220	PDBbind-CN: -logKd/Ki=4.00,IC50=100uM BindingDB: IC50=100000nM

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

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