Structure of PDB 6fe3 Chain A Binding Site BS01

Receptor Information

>6fe3 Chain A (length=333) Species: 5691 (Trypanosoma brucei)

VTAITKVEREAVLVCELPSFDVTDVEFDLFRARESTDKPLDVAAAIAYRL
LLGSGLPQKFGCSDEVLLNFILQCRKKYRNVPYHNFYHVVDVCQTIHTFL
YRGNVYEKLTELECFVLLITALVHDLDHMGLNNSFYLKTESPLGILSSAS
GNTSVLEVHHCNLAVEILSDPESDVFDGLEGAERTLAFRSMIDCVLATDM
AKHGSALEAFLASAADQSSDEAAFHRMTMEIILKAGDISNVTKPFDISRQ
WAMAVTEEFYRQGDMEKERGVEVLPMFDRSKNMELAKGQIGFIDFVAAPF
FQKIVDACLQGMQWTVDRIKSNRAQWERVLETR

Ligand information

• Ligand ID: D68
• InChI: InChI=1S/C30H34F4N4O6/c1-30(2)14-23(39)37(24(40)15-30)16-25(41)36-11-9-18(10-12-36)38-27(42)20-6-4-3-5-19(20)26(35-38)17-7-8-21(43-28(31)32)22(13-17)44-29(33)34/h3-4,7-8,13,18-20,28-29H,5-6,9-12,14-16H2,1-2H3/t19-,20+/m0/s1
• InChIKey: WVAQTVIALKSAMT-VQTJNVASSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC1(CC(=O)N(C(=O)C1)CC(=O)N2CCC(CC2)N3C(=O)C4CC=CCC4C(=N3)c5ccc(c(c5)OC(F)F)OC(F)F)C
  CACTVS 3.385: CC1(C)CC(=O)N(CC(=O)N2CCC(CC2)N3N=C([CH]4CC=CC[CH]4C3=O)c5ccc(OC(F)F)c(OC(F)F)c5)C(=O)C1
  OpenEye OEToolkits 2.0.6: CC1(CC(=O)N(C(=O)C1)CC(=O)N2CCC(CC2)N3C(=O)[C@@H]4CC=CC[C@@H]4C(=N3)c5ccc(c(c5)OC(F)F)OC(F)F)C
  CACTVS 3.385: CC1(C)CC(=O)N(CC(=O)N2CCC(CC2)N3N=C([C@H]4CC=CC[C@H]4C3=O)c5ccc(OC(F)F)c(OC(F)F)c5)C(=O)C1
• Formula: C30 H34 F4 N4 O6
• Name: 1-(2-{4-[(4aS,8aR)-4-[3,4-bis(difluoromethoxy)phenyl]-1-oxo-1,2,4a,5,8,8a-hexahydrophthalazin-2-yl]piperidin-1-yl}-2-oxoethyl)-4,4-dimethylpiperidine-2,6-dione
• ChEMBL: CHEMBL4530777
• PDB chain: 6fe3 Chain A Residue 1003

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6fe3 TbrPDEB1 structure with inhibitor NPD-1439
• Resolution: 1.62 Å
• Binding residue (original residue number in PDB): M785 N825 A837 M861 Q874 G876 F877 F880
• Binding residue (residue number reindexed from 1): M200 N240 A252 M276 Q289 G291 F292 F295
• Annotation score: 1
• Binding affinity: BindingDB: Ki=407nM

Enzymatic activity

• Enzyme Commision number: 3.1.4.-

Gene Ontology

Molecular Function

• GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity
• GO:0008081 phosphoric diester hydrolase activity

Biological Process

• GO:0007165 signal transduction

External links

• PDB: RCSB:6fe3, PDBe:6fe3, PDBj:6fe3
• PDBsum: 6fe3
• UniProt: Q8WQX9