Structure of PDB 1rts Chain A Binding Site BS02

Receptor Information

>1rts Chain A (length=280) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

QHGELQYLRQVEHIMRCGFKKEDRTGTGTLSVFGMQARYSLRDEFPLLTT
KRVFWKGVLEELLWFIKGSTNAKELSSKGVRIWDANGSRDFLDSLGFSAR
QEGDLGPVYGFQWRHFGADYKDMDSDYSGQGVDQLQKVIDTIKTNPDDRR
IIMCAWNPKDLPLMALPPCHALCQFYVVNGELSCQLYQRSGDMGLGVPFN
IASYALLTYMIAHITGLQPGDFVHTLGDAHIYLNHIEPLKIQLQREPRPF
PKLRILRKVETIDDFKVEDFQIEGYNPHPT

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

PDB chain

1rts Chain A Residue 309 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	1rts Crystal structures of rat thymidylate synthase inhibited by Tomudex, a potent anticancer drug.
Resolution	3.3 Å
Binding residue (original residue number in PDB)	F74 I102 W103 D212 L215 G216 F219 Y252
Binding residue (residue number reindexed from 1)	F54 I82 W83 D192 L195 G196 F199 Y232
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	E81 W103 Y129 C189 R209 D212
Catalytic site (residue number reindexed from 1)	E61 W83 Y109 C169 R189 D192
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
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:1rts, PDBe:1rts, PDBj:1rts
PDBsum	1rts
PubMed	9894005
UniProt	P45352\|TYSY_RAT Thymidylate synthase (Gene Name=Tyms)

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