Structure of PDB 4e10 Chain A Binding Site BS03

Receptor Information

>4e10 Chain A (length=318) Species: 176299 (Agrobacterium fabrum str. C58)

PKTGVATSIVEKIERAEFNTAGRKPTVLLRIADFIAAMNGMDAKQDMQAL
WDAEIAIMNGRAQTTIISYITKYRNAIREAFGDDHPMLKIATGDAAMADE
ARRVKMEKIANKHGALITFENYRQVLKICEDCLKSSDPLMIGIGLIGMTG
RRPYEVFTQAEFSPAPYGKGVSKWSILFNGQAKTKQGEGTKFGITYEIPV
LTRSETVLAAYKRLRESGQGKLWHGMSIDDFSSETRLLLRDTVFNLFEDV
WPKEELPKPYGLRHLYAEVAYHNFAPPHVTKNSYFAAILGHNNNDLETSL
SYMTYTLPEDRDNALARL

Ligand information

• Ligand ID: DT
• 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'-MONOPHOSPHATE
• ChEMBL: CHEMBL394429
• DrugBank: DB01643
• ZINC: ZINC000001678872
• PDB chain: 4e10 Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4e10 An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation.
• Resolution: 2.506 Å
• Binding residue (original residue number in PDB): K208 T401
• Binding residue (residue number reindexed from 1): K105 T298
• Annotation score: 4

External links

• PDB: RCSB:4e10, PDBe:4e10, PDBj:4e10
• PDBsum: 4e10
• PubMed: 23382649
• UniProt: Q7CWV1