Structure of PDB 5j7w Chain D Binding Site BS01

Receptor Information
>5j7w Chain D (length=315) Species: 1351 (Enterococcus faecalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEEAYLALGKKILEEGHFKEDRTGTGTYSLFGYQMRFDLAKGFPLLTTKR
VPFGLIKSELLWFLKGDTNIRYLLERNNHIWDEWAFERYVKSADYQGPDM
TDFGHRVLQDPAFAEQYKEEHQKFCDAILNDAEFAEKYGELGNIYGAQWR
HWETKDGSFIDQLANVIEMIKTNPDSRRLIVSAWNPEDVPSMALPPCHTM
FQFYVNEGKLSCQLYQRSADVFLGVPFNIASYALLTHLIAHETGLEVGEF
VHTLGDAHLYQNHVEQMQEQLSREVRSFPTLVLNPDKASVFDFDMEDIKV
EGYDPHPTIKAPIAV
Ligand information
Ligand IDMTX
InChIInChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)/t13-/m0/s1
InChIKeyFBOZXECLQNJBKD-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O
CACTVS 3.341CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O
OpenEye OEToolkits 1.5.0CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)NC(CCC(=O)O)C(=O)O
ACDLabs 10.04O=C(O)C(NC(=O)c1ccc(cc1)N(C)Cc2nc3c(nc2)nc(nc3N)N)CCC(=O)O
OpenEye OEToolkits 1.5.0CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@H](CCC(=O)O)C(=O)O
FormulaC20 H22 N8 O5
NameMETHOTREXATE
ChEMBLCHEMBL34259
DrugBankDB00563
ZINCZINC000001529323
PDB chain5j7w Chain D Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5j7w X-ray crystal structures of Enterococcus faecalis thymidylate synthase with folate binding site inhibitors.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		L55 I80 W81 W84 D220 L223 G224 F227 Y260 I313 A314
Binding residue
(residue number reindexed from 1)		L55 I80 W81 W84 D220 L223 G224 F227 Y260 I313 A314
Annotation score2
Binding affinityMOAD: Ki=13uM
PDBbind-CN: -logKd/Ki=4.89,Ki=13uM
Enzymatic activity
Catalytic site (original residue number in PDB) E59 W81 Y145 C197 R217 D220
Catalytic site (residue number reindexed from 1) E59 W81 Y145 C197 R217 D220
Enzyme Commision number 2.1.1.45: thymidylate synthase.
Gene Ontology
Molecular Function
GO:0004799 thymidylate synthase activity
GO:0008168 methyltransferase activity
GO:0016741 transferase activity, transferring one-carbon groups
Biological Process
GO:0006231 dTMP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0009165 nucleotide biosynthetic process
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm
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:5j7w, PDBe:5j7w, PDBj:5j7w
PDBsum5j7w
PubMed27517810
UniProtQ834R3|TYSY_ENTFA Thymidylate synthase (Gene Name=thyA)

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