Structure of PDB 1hvy Chain D Binding Site BS02
Receptor Information
>1hvy Chain D (length=288) Species:
9606
(Homo sapiens) [
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PPHGELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLT
TKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFST
REEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDR
RIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPF
NIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRP
FPKLRILRKVEKIDDFKAEDFQIEGYNPHPTIKMEMAV
Ligand information
Ligand ID
D16
InChI
InChI=1S/C21H22N4O6S/c1-11-22-14-4-3-12(9-13(14)19(28)23-11)10-25(2)17-7-6-16(32-17)20(29)24-15(21(30)31)5-8-18(26)27/h3-4,6-7,9,15H,5,8,10H2,1-2H3,(H,24,29)(H,26,27)(H,30,31)(H,22,23,28)/t15-/m0/s1
InChIKey
IVTVGDXNLFLDRM-HNNXBMFYSA-N
SMILES
Software
SMILES
ACDLabs 12.01
O=C(c3sc(N(C)Cc2ccc1NC(=NC(=O)c1c2)C)cc3)NC(C(=O)O)CCC(=O)O
CACTVS 3.370
CN(Cc1ccc2NC(=NC(=O)c2c1)C)c3sc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6
CC1=NC(=O)c2cc(ccc2N1)CN(C)c3ccc(s3)C(=O)N[C@@H](CCC(=O)O)C(=O)O
CACTVS 3.370
CN(Cc1ccc2NC(=NC(=O)c2c1)C)c3sc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6
CC1=NC(=O)c2cc(ccc2N1)CN(C)c3ccc(s3)C(=O)NC(CCC(=O)O)C(=O)O
Formula
C21 H22 N4 O6 S
Name
TOMUDEX;
ZD1694;
Raltitrexed
ChEMBL
CHEMBL225071
DrugBank
DB00293
ZINC
ZINC000003832372
PDB chain
1hvy Chain D Residue 417 [
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Receptor-Ligand Complex Structure
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PDB
1hvy
Human thymidylate synthase is in the closed conformation when complexed with dUMP and raltitrexed, an antifolate drug
Resolution
1.9 Å
Binding residue
(original residue number in PDB)
F80 I108 W109 N112 D218 G222 F225 Y258 M311
Binding residue
(residue number reindexed from 1)
F55 I83 W84 N87 D193 G197 F200 Y233 M286
Annotation score
1
Binding affinity
BindingDB: IC50=29000nM
Enzymatic activity
Catalytic site (original residue number in PDB)
E87 W109 Y135 C195 R215 D218
Catalytic site (residue number reindexed from 1)
E62 W84 Y110 C170 R190 D193
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
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Biological Process
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Cellular Component
External links
PDB
RCSB:1hvy
,
PDBe:1hvy
,
PDBj:1hvy
PDBsum
1hvy
PubMed
11329255
UniProt
P04818
|TYSY_HUMAN Thymidylate synthase (Gene Name=TYMS)
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