Structure of PDB 4eb4 Chain C Binding Site BS03
Receptor Information
>4eb4 Chain C (length=295) Species:
10090
(Mus musculus) [
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MLVVGSELQSDAQRHGELQYLRQVEHILRCGFKKEDRTGTGTLSVFGMQA
RYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVRIWDANG
SRDFLDSLGFSARQEGDLGPVYGFQWRHFGAEYKDMDSDYSGQGVDQLQK
VIDTIKTNPDDRRIIMCAWNPKDLPLMALPPCHALCQFYVVNGELSCQLY
QRSGDMGLGVPFNIASYALLTYMIAHITGLQPGDFVHTLGDAHIYLNHIE
PLKIQLQREPRPFPKLKILRKVETIDDFKVEDFQIEGYNPHPTIK
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
Software
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
4eb4 Chain D Residue 401 [
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Receptor-Ligand Complex Structure
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PDB
4eb4
Crystal structure of mouse thymidylate synthase in tertiary complex with dUMP and raltitrexed reveals N-terminus architecture and two different active site conformations.
Resolution
1.74 Å
Binding residue
(original residue number in PDB)
R169 R170
Binding residue
(residue number reindexed from 1)
R162 R163
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)
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
View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB
RCSB:4eb4
,
PDBe:4eb4
,
PDBj:4eb4
PDBsum
4eb4
PubMed
24995339
UniProt
P07607
|TYSY_MOUSE Thymidylate synthase (Gene Name=Tyms)
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