Structure of PDB 5t6b Chain D Binding Site BS03

Receptor Information

>5t6b Chain D (length=393) Species: 46161 (Actinomadura kijaniata)

ARCRVCGDTVDEFLDLGRQPLSDRFLTPADTDGEFFYRLAVGRCHACGMV
QLTEEVPRHLMFSVMREHFAMVARDFLATELTGPDPFVVEIGCNDGIMLR
AVHEAGVRHLGFEPSAGVAEVARSRGVRVRTEFFEKATATAVRESEGPAD
VIYAANTMCHIPYLESVFQGADALLGPDGVVVFEDPYLGDIVAKTSFDQI
YDEHFYLFSAGSVAAMAERFGFELVDVERLPVHGGEVRYTLARRGARTPT
EAVGRLLAEEREQGLDDLATLRTFAANVHTVRDELVALLTRLRAEGHRVV
GYGATAKSATVTNFCGIGPDLVSFVCDTTPGKQHRLTPGKHLPVRPAEAF
ADPYPDYALLFAWNHAEEIMAKEQEFHQAGGRWILYVPEVHIR

Ligand information

• Ligand ID: TMP
• InChI: InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
• InChIKey: GYOZYWVXFNDGLU-XLPZGREQSA-N
• SMILES:
  CACTVS 3.341: CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
  CACTVS 3.341: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
  ACDLabs 10.04: O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O
• Formula: C10 H15 N2 O8 P
• Name: THYMIDINE-5'-PHOSPHATE
• ChEMBL: CHEMBL394429
• DrugBank: DB01643
• ZINC: ZINC000001678872
• PDB chain: 5t6b Chain D Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5t6b Structural studies on KijD1, a sugar C-3'-methyltransferase.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): D348 T349 K353 H386 K393
• Binding residue (residue number reindexed from 1): D327 T328 K332 H365 K372
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0016740 transferase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:5t6b, PDBe:5t6b, PDBj:5t6b
• PDBsum: 5t6b
• PubMed: 27595766
• UniProt: B3TMQ9