Structure of PDB 3um5 Chain B Binding Site BS03

Receptor Information
>3um5 Chain B (length=544) Species: 5833 (Plasmodium falciparum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVCDVFDIYAICVCCKVESKNEGKKNEVFNNYTFRGLGNKGVLPWKCNSL
DMKYFCAVTTYVNESKYEKLKYKRCKYLNKETVKLQNVVVMGRTTWESIP
KKFKPLSNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFI
IGGSVVYQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDV
YTSNNTTLDFIIYKKTNNDDEEEDDFVYFNFNKEKEEKNKNSIHPNDFQI
YNSLKYKYHPEYQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQ
YFPLLTTKKLFLRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLD
NRKLFHREVNDLGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIK
NDPTSRRILLCAWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDL
GLGVPFNIASYSIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQL
NRIPYPFPTLKLNPDIKNIEDFTISDFTIQNYVHHEKISMDMAA
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain3um5 Chain B Residue 710 [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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PDB3um5 Combined Spatial Limitation around Residues 16 and 108 of Plasmodium falciparum Dihydrofolate Reductase Explains Resistance to Cycloguanil.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		C15 V16 L40 G44 V45 L46 G105 R106 T107 T108 L127 S128 R129 N144 I164 G165 G166 S167 V168 V169 Y170 E172
Binding residue
(residue number reindexed from 1)		C12 V13 L37 G41 V42 L43 G92 R93 T94 T95 L114 S115 R116 N131 I151 G152 G153 S154 V155 V156 Y157 E159
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) L46 D54 E382 W404 Y430 C490 R510 D513
Catalytic site (residue number reindexed from 1) L43 D51 E318 W340 Y366 C426 R446 D449
Enzyme Commision number 1.5.1.3: dihydrofolate reductase.
2.1.1.45: thymidylate synthase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
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:3um5, PDBe:3um5, PDBj:3um5
PDBsum3um5
PubMed22526319
UniProtA7UD81

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