Structure of PDB 2pak Chain B Binding Site BS02

Receptor Information

>2pak Chain B (length=134) Species: 143495 (Aneurinibacillus thermoaerophilus)

ENKVINFKKIIDSRGSLVAIEENKNIPFSIKRVYYIFDTKGEEPRGFHAN
KKLEQVLVCLNGSCRVILDDGNIIQEITLDSPAVGLYVGPAVWHEMHDFS
SDCVMMVLASDYYDETDYIRQYDNFKKYIAKINL

Ligand information

• Ligand ID: TYD
• InChI: InChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
• InChIKey: UJLXYODCHAELLY-XLPZGREQSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
  CACTVS 3.341: CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
  CACTVS 3.341: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
• Formula: C10 H16 N2 O11 P2
• Name: THYMIDINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL259724
• DrugBank: DB03103
• ZINC: ZINC000008215882
• PDB chain: 2pak Chain B Residue 140

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2pak The X-ray Structure of dTDP-4-Keto-6-deoxy-D-glucose-3,4-ketoisomerase.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): R33 Y35 Y114
• Binding residue (residue number reindexed from 1): R32 Y34 Y113
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 5.3.2.3: TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase (dTDP-3-dehydro-6- deoxy-alpha-D-galactopyranose-forming).

Gene Ontology

Molecular Function

• GO:0016853 isomerase activity

External links

• PDB: RCSB:2pak, PDBe:2pak, PDBj:2pak
• PDBsum: 2pak
• PubMed: 17459872
• UniProt: Q6T1W8|FDTA_ANETH TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase (Gene Name=fdtA)