Structure of PDB 4eb4 Chain D Binding Site BS01

Receptor Information
>4eb4 Chain D (length=297) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLVVGSELQSDAQRHGELQYLRQVEHILRCGFKKEDRTGTGTLSVFGMQA
RYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVRIWDANG
SRDFLDSLGFSARQEGDLGPVYGFQWRHFGAEYKDMDSDYSGQGVDQLQK
VIDTIKTNPDDRRIIMCAWNPKDLPLMALPPCHALCQFYVVNGELSCQLY
QRSGDMGLGVPFNIASYALLTYMIAHITGLQPGDFVHTLGDAHIYLNHIE
PLKIQLQREPRPFPKLKILRKVETIDDFKVEDFQIEGYNPHPTIKME
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 chain4eb4 Chain C Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4eb4 Crystal structure of mouse thymidylate synthase in tertiary complex with dUMP and raltitrexed reveals N-terminus architecture and two different active site conformations.
Resolution1.74 Å
Binding residue
(original residue number in PDB)		R169 R170
Binding residue
(residue number reindexed from 1)		R162 R163
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) E81 W103 Y129 C189 R209 D212
Catalytic site (residue number reindexed from 1) E74 W96 Y122 C182 R202 D205
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:0097421 liver regeneration
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4eb4, PDBe:4eb4, PDBj:4eb4
PDBsum4eb4
PubMed24995339
UniProtP07607|TYSY_MOUSE Thymidylate synthase (Gene Name=Tyms)

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