Structure of PDB 3h9k Chain D Binding Site BS01

Receptor Information

>3h9k Chain D (length=280) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

PHGELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTT
KRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTR
EEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQKVIDTIKTNPDDRR
IIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFN
IASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPF
PKLRILRKVEKIDDFKAEDFQIEGYNPHPT

Ligand information

Ligand ID

UFP

InChI

InChI=1S/C9H12FN2O8P/c10-4-2-12(9(15)11-8(4)14)7-1-5(13)6(20-7)3-19-21(16,17)18/h2,5-7,13H,1,3H2,(H,11,14,15)(H2,16,17,18)/t5-,6+,7+/m0/s1

InChIKey

HFEKDTCAMMOLQP-RRKCRQDMSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	C1C(C(OC1N2C=C(C(=O)NC2=O)F)COP(=O)(O)O)O
OpenEye OEToolkits 1.5.0	C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)F)COP(=O)(O)O)O
CACTVS 3.341	O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(F)C(=O)NC2=O
ACDLabs 10.04	FC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O
CACTVS 3.341	O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(F)C(=O)NC2=O

Formula

C9 H12 F N2 O8 P

Name

5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

PDB chain

3h9k Chain D Residue 565 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	3h9k Structures of human thymidylate synthase R163K with dUMP, FdUMP and glutathione show asymmetric ligand binding.
Resolution	2.65 Å
Binding residue (original residue number in PDB)	R50 C195 Q214 R215 S216 N226
Binding residue (residue number reindexed from 1)	R24 C169 Q188 R189 S190 N200
Annotation score	3
Binding affinity	BindingDB: Ki=14nM

Enzymatic activity

Catalytic site (original residue number in PDB)	E87 W109 Y135 C195 R215 D218
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: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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:3h9k, PDBe:3h9k, PDBj:3h9k
PDBsum	3h9k
PubMed	21206062
UniProt	P04818\|TYSY_HUMAN Thymidylate synthase (Gene Name=TYMS)

[Back to BioLiP]