Structure of PDB 4ud9 Chain H Binding Site BS03

Receptor Information

>4ud9 Chain H (length=254) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTA
GQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGD
SGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVI
DQFG

Ligand information

• Ligand ID: FQI
• InChI: InChI=1S/C5H4ClNOS/c6-4-2-1-3(9-4)5(7)8/h1-2H,(H2,7,8)
• InChIKey: OMOBWMBJNNCUFO-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: O=C(N)c1sc(Cl)cc1
  OpenEye OEToolkits 1.7.6: c1cc(sc1C(=O)N)Cl
  CACTVS 3.385: NC(=O)c1sc(Cl)cc1
• Formula: C5 H4 Cl N O S
• Name: 5-CHLORO-2-THIOPHENECARBOXAMIDE
• ChEMBL: CHEMBL3608990
• ZINC: ZINC000002753342
• PDB chain: 4ud9 Chain H Residue 1257

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ud9 Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why.
• Resolution: 1.124 Å
• Binding residue (original residue number in PDB): D189 A190 C191 E192 V213 W215 G216 G219 G226 F227
• Binding residue (residue number reindexed from 1): D195 A196 C197 E198 V221 W223 G224 G226 G234 F235
• Annotation score: 1
• Binding affinity: MOAD: Kd=475uM
  BindingDB: Kd=507000nM,Ki=431000nM

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:4ud9, PDBe:4ud9, PDBj:4ud9
• PDBsum: 4ud9
• PubMed: 26270568
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)