Structure of PDB 6pf3 Chain B Binding Site BS01

Receptor Information
>6pf3 Chain B (length=285) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKR
VFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREE
GDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDRRII
MCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNIA
SYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPK
LRILRKVEKIDDFKAEDFQIEGYNPHPTIKMEMAV
Ligand information
Ligand IDUMP
InChIInChI=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
InChIKeyJSRLJPSBLDHEIO-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
FormulaC9 H13 N2 O8 P
Name2'-DEOXYURIDINE 5'-MONOPHOSPHATE;
DUMP
ChEMBLCHEMBL211312
DrugBankDB03800
ZINCZINC000004228260
PDB chain6pf3 Chain B Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6pf3 Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors.
Resolution2.391 Å
Binding residue
(original residue number in PDB)		R50 C195 Q214 R215 S216 D218 N226 H256 Y258
Binding residue
(residue number reindexed from 1)		R22 C167 Q186 R187 S188 D190 N198 H228 Y230
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) E87 W109 Y135 C195 R215 D218
Catalytic site (residue number reindexed from 1) E59 W81 Y107 C167 R187 D190
Enzyme Commision number 2.1.1.45: thymidylate synthase.
Gene Ontology
Molecular Function
GO:0000900 mRNA regulatory element binding translation repressor activity
GO:0003729 mRNA binding
GO:0004799 thymidylate synthase activity
GO:0005542 folic acid binding
GO:0008168 methyltransferase activity
GO:0016741 transferase activity, transferring one-carbon groups
GO:0042803 protein homodimerization activity
GO:1901363 heterocyclic compound binding
GO:1990825 sequence-specific mRNA binding
Biological Process
GO:0006206 pyrimidine nucleobase metabolic process
GO:0006231 dTMP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0006417 regulation of translation
GO:0007623 circadian rhythm
GO:0009165 nucleotide biosynthetic process
GO:0009410 response to xenobiotic stimulus
GO:0009636 response to toxic substance
GO:0014070 response to organic cyclic compound
GO:0017148 negative regulation of translation
GO:0019860 uracil metabolic process
GO:0032259 methylation
GO:0032570 response to progesterone
GO:0033189 response to vitamin A
GO:0034097 response to cytokine
GO:0035999 tetrahydrofolate interconversion
GO:0045471 response to ethanol
GO:0046653 tetrahydrofolate metabolic process
GO:0046683 response to organophosphorus
GO:0048589 developmental growth
GO:0051216 cartilage development
GO:0051384 response to glucocorticoid
GO:0051593 response to folic acid
GO:0060574 intestinal epithelial cell maturation
GO:0071897 DNA biosynthetic process
GO:0097421 liver regeneration
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix
GO:0005829 cytosol

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:6pf3, PDBe:6pf3, PDBj:6pf3
PDBsum6pf3
PubMed31536894
UniProtP04818|TYSY_HUMAN Thymidylate synthase (Gene Name=TYMS)

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