Structure of PDB 7ed6 Chain B Binding Site BS03

Receptor Information

>7ed6 Chain B (length=196) Species: 300852 (Thermus thermophilus HB8)

EAWGPEAVAEAFRYATRWFQVYVEELNALNVYPVPDGDTGTNMLHTLEAA
RRELDLADTSRMDQVARALAYGSLLGARGNSGVILSQILRGFAEALKGKR
ALDGSLLRRALRMGAESGYKAVMRPVEGTILTVARAAGEGARGEALEEVL
ETALEAAREALERTPELLPVLRQAGVVDAGGAGYVRLLEGMRGYAL

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 7ed6 Chain B Residue 203

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ed6 Crystal structure of a nucleotide-binding domain of fatty acid kinase FakA from Thermus thermophilus HB8.
• Resolution: 1.9285 Å
• Binding residue (original residue number in PDB): N32 Y34 P35 D38 D40 T41 G81 N82 S83 I86 V128 T131 L133 D180 G182
• Binding residue (residue number reindexed from 1): N30 Y32 P33 D36 D38 T39 G79 N80 S81 I84 V126 T129 L131 D178 G180
• Annotation score: 5

Gene Ontology

Molecular Function

• GO:0004371 glycerone kinase activity

Biological Process

• GO:0006071 glycerol metabolic process

External links

• PDB: RCSB:7ed6, PDBe:7ed6, PDBj:7ed6
• PDBsum: 7ed6
• PubMed: 36228973
• UniProt: Q5SLS9