Structure of PDB 1dx5 Chain M Binding Site BS01

Receptor Information

>1dx5 Chain M (length=259) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFIENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTA
NVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDA
CEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWI
QKVIDQFGE

Ligand information

• Ligand ID: 0GJ
• InChI: InChI=1S/C14H27ClN6O5/c15-6-10(22)9(2-1-5-19-14(17)18)21-11(23)7-20-13(26)8(16)3-4-12(24)25/h8-10,22H,1-7,16H2,(H,20,26)(H,21,23)(H,24,25)(H4,17,18,19)/p+1/t8-,9-,10+/m0/s1
• InChIKey: XELWNHKFCNMWQO-LPEHRKFASA-O
• SMILES:
  CACTVS 3.370: N[CH](CCC(O)=O)C(=O)NCC(=O)N[CH](CCCNC(N)=[NH2+])[CH](O)CCl
  CACTVS 3.370: N[C@@H](CCC(O)=O)C(=O)NCC(=O)N[C@@H](CCCNC(N)=[NH2+])[C@H](O)CCl
  ACDLabs 12.01: O=C(NC(CCCNC(=[NH2+])\N)C(O)CCl)CNC(=O)C(N)CCC(=O)O
  OpenEye OEToolkits 1.7.0: C(CC(C(CCl)O)NC(=O)CNC(=O)C(CCC(=O)O)N)CNC(=[NH2+])N
  OpenEye OEToolkits 1.7.0: C(C[C@@H]([C@@H](CCl)O)NC(=O)CNC(=O)[C@H](CCC(=O)O)N)CNC(=[NH2+])N
• Formula: C14 H28 Cl N6 O5
• Name: L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide
• PDB chain: 1dx5 Chain M Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1dx5 Structural Basis for the Anticoagulant Activity of the Thrombin-Thrombomodulin Complex
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): W215 G216
• Binding residue (residue number reindexed from 1): W227 G228
• Annotation score: 1

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

External links

• PDB: RCSB:1dx5, PDBe:1dx5, PDBj:1dx5
• PDBsum: 1dx5
• PubMed: 10761923
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)