Structure of PDB 7f3y Chain A Binding Site BS04

Receptor Information
>7f3y Chain A (length=547) Species: 5833 (Plasmodium falciparum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MMEQVCDVFDIYAICACCKVESKNEGKKNEVFNNYTFRGLGNKGVLPWKC
NSLDMKYFCAVTTYVNESKYEKLKYKRCKYLNKETKKLQNVVVMGRTSWE
SIPKKFKPLSNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYK
CFIIGGSVVYQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISV
SDVYTSNNTTLDFIIYKKTNNDDEEEDDFVYFNFNKEKEEKNKNSIHPND
FQIYNSLKYKYHPEYQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFD
LSQYFPLLTTKKLFLRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTRE
FLDNRKLFHREVNDLGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIIN
LIKNDPTSRRILLCAWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRS
CDLGLGVPFNIASYSIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLK
IQLNRIPYPFPTLKLNPDIKNIEDFTISDFTIQNYVHHEKISMDMAA
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 chain7f3y Chain A Residue 704 [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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PDB7f3y MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances.
Resolution2.252 Å
Binding residue
(original residue number in PDB)		D513 L516 G517 F520 Y553 I602 S603
Binding residue
(residue number reindexed from 1)		D452 L455 G456 F459 Y492 I541 S542
Annotation score2
Binding affinityBindingDB: IC50=84nM
Enzymatic activity
Enzyme Commision number 1.5.1.3: dihydrofolate reductase.
2.1.1.45: thymidylate synthase.
Gene Ontology
Molecular Function
GO:0004146 dihydrofolate reductase activity
GO:0004799 thymidylate synthase activity
GO:0008168 methyltransferase activity
GO:0016491 oxidoreductase activity
GO:0016741 transferase activity, transferring one-carbon groups
Biological Process
GO:0006231 dTMP biosynthetic process
GO:0006730 one-carbon metabolic process
GO:0009165 nucleotide biosynthetic process
GO:0032259 methylation
GO:0046654 tetrahydrofolate biosynthetic process
Cellular Component
GO:0005739 mitochondrion
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:7f3y, PDBe:7f3y, PDBj:7f3y
PDBsum7f3y
PubMed34614393
UniProtP13922|DRTS_PLAFK Bifunctional dihydrofolate reductase-thymidylate synthase

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