Structure of PDB 6pfh Chain A Binding Site BS01

Receptor Information
>6pfh Chain A (length=508) Species: 237895 (Cryptosporidium hominis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKNVSIVVAASVLSSGIGINGQLPWSISEDLKFFSKITNNKCDSNKKNAL
IMGRKTWDSIGRRPLKNRIIVVISSSLPQDEADPNVVVFRNLEDSIENLM
NDDSIENIFVCGGESIYRDALKDNFVDRIYLTRVALEDIEFDTYFPEIPE
TFLPVYMSQTFCTKNISYDFMIFEKQEKKLKSIDDTVDLLGEIFGIRKMG
NRHKFPKEEIYNTPSIRFGREHYEFQYLDLLSRVLENGAYRENRTGISTY
SIFGQMMRFDMRESFPLLTTKKVAIRSIFEELIWFIKGDTNGNHLIEKKV
YIWSGNGSKEYLERIGLGHREENDLGPIYGFQWRHYNGEYKTMHDDYTGV
GVDQLAKLIETLKNNPKDRRHILTAWNPSALSQMALPPCHVLSQYYVTND
NCLSCNLYQRSCDLGLGSPFNIASYAILTMMLAQVCGYEPGELAIFIGDA
HIYENHLTQLKEQLSRTPRPFPQLKFKRKVENIEDFKWEDIELIGYYPYP
TIKMDMAV
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 chain6pfh Chain A Residue 601 [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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PDB6pfh Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors.
Resolution2.94 Å
Binding residue
(original residue number in PDB)		V10 A11 I19 G23 Q24 L25 G55 R56 K57 T58 I75 S76 S77 R92 C113 G114 G115 E116 S117
Binding residue
(residue number reindexed from 1)		V8 A9 I17 G21 Q22 L23 G53 R54 K55 T56 I73 S74 S75 R90 C111 G112 G113 E114 S115
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) L25 D32 E294 W316 Y342 C402 R423 D426
Catalytic site (residue number reindexed from 1) L23 D30 E281 W303 Y329 C389 R410 D413
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6pfh, PDBe:6pfh, PDBj:6pfh
PDBsum6pfh
PubMed31536894
UniProtA0A0S4TER9

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