Structure of PDB 5by6 Chain B Binding Site BS02

Receptor Information

>5by6 Chain B (length=288) Species: 6334 (Trichinella spiralis)

DYVNQEELNYLNQLKDIIDHGVRKNDRTGIGTLSTFGTQSRYCLRDDIFP
LLTTKRVFWRGVVEELLWFISGSTNAKQLSEKNVNIWDGNSSREFLDSRG
LYNYEEGDLGPVYGFQWRHFGCPYSSMTADYKGKGYDQLQQCIKMIREEP
ESRRIIMTAWNPCDLEKVALPPCHCFVQFYVADGELSCQMYQRSADMGLG
VPFNIASYSLLTRMIAHITSLKPGFFIHTIGDAHVYLTHVDALKVQMERK
PRPFPKLKILRNVENIDDFRAEDFELINYKPYPKISMP

Ligand information

• Ligand ID: UMP
• InChI: InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
• InChIKey: JSRLJPSBLDHEIO-SHYZEUOFSA-N
• SMILES:
  ACDLabs 12.01: O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
  CACTVS 3.370: O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.7.6: C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
  CACTVS 3.370: O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.7.6: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
• Formula: C9 H13 N2 O8 P
• Name: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE;
  DUMP
• ChEMBL: CHEMBL211312
• DrugBank: DB03800
• ZINC: ZINC000004228260
• PDB chain: 5by6 Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5by6 Crystal structures of nematode (parasitic T. spiralis and free living C. elegans), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in search for nematode-specific inhibitors of TS.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): R43 C189 Q208 R209 S210 D212 N220 H250 Y252
• Binding residue (residue number reindexed from 1): R27 C173 Q192 R193 S194 D196 N204 H234 Y236
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): E81 W103 Y129 C189 R209 D212
• Catalytic site (residue number reindexed from 1): E65 W87 Y113 C173 R193 D196
• Enzyme Commision number: 2.1.1.45: thymidylate synthase.

Gene Ontology

Molecular Function

• GO:0004799 thymidylate synthase activity
• GO:0008168 methyltransferase activity
• GO:0016741 transferase activity, transferring one-carbon groups

Biological Process

• GO:0006231 dTMP biosynthetic process
• GO:0006235 dTTP biosynthetic process
• GO:0009165 nucleotide biosynthetic process
• GO:0032259 methylation

Cellular Component

• GO:0005739 mitochondrion
• GO:0005829 cytosol

External links

• PDB: RCSB:5by6, PDBe:5by6, PDBj:5by6
• PDBsum: 5by6
• PubMed: 28826032
• UniProt: Q9NDD3