Structure of PDB 6kp7 Chain B Binding Site BS03

Receptor Information
>6kp7 Chain B (length=533) Species: 5833 (Plasmodium falciparum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CDVFDIYAICACCKVESKNEGKKNEVFNNYTFRGLGNKGVLPWKCISLDM
KYFRAVTTYVNESKYEKLKYKRCKYLNKNSKKLQNVVVMGRTNWESIPKK
FKPLSNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFILG
GSVVYQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYT
SNNTTLDFIIYKKTDDEEEDDFVYFNFNKENKNSIHPNDFQIYNSLKYKY
HPEYQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTK
KLFLRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHRE
VNDLGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRI
LLCAWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNI
ASYSIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFP
TLKLNPDIKNIEDFTISDFTIQNYVHHEKISMD
Ligand information
Ligand IDUMP
InChIInChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyJSRLJPSBLDHEIO-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
FormulaC9 H13 N2 O8 P
Name2'-DEOXYURIDINE 5'-MONOPHOSPHATE;
DUMP
ChEMBLCHEMBL211312
DrugBankDB03800
ZINCZINC000004228260
PDB chain6kp7 Chain B Residue 702 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6kp7 6-Hydrophobic aromatic substituent pyrimethamine analogues as potential antimalarials for pyrimethamine-resistant Plasmodium falciparum.
Resolution1.97 Å
Binding residue
(original residue number in PDB)
R345 C490 H491 Q509 R510 S511 D513 N521 H551 Y553
Binding residue
(residue number reindexed from 1)
R273 C418 H419 Q437 R438 S439 D441 N449 H479 Y481
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) L46 D54 E382 W404 Y430 C490 R510 D513
Catalytic site (residue number reindexed from 1) L41 D49 E310 W332 Y358 C418 R438 D441
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:6kp7, PDBe:6kp7, PDBj:6kp7
PDBsum6kp7
PubMed31685330
UniProtD9N170

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