Structure of PDB 6a2k Chain B Binding Site BS04

Receptor Information
>6a2k Chain B (length=527) Species: 5833 (Plasmodium falciparum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VCDVFDIYAICACCKVESNEVFNNYTFRGLGNKGVLPWKCNSLDMKYFCA
VTTYVNESKYEKLKYKRCKYLNKKKLQNVVVMGRTSWESIPKKFKPLSNR
INVILSRTLKKEDDVYIINKVEDLIVLLGKLNYYKCFIIGGSVVYQEFLE
KKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNTTLDFII
YKKTNDEEEDDFVYFNFNKEKNKNSIHPNDFQIYNSLKYKYHPEYQYLNI
IYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLFLRGIIE
ELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVNDLGPIYG
FQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLCAWNVKD
LDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASYSIFTHM
IAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLKLNPDIK
NIEDFTISDFTIQNYVHHEKISMDMAA
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 chain6a2k Chain B Residue 703 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6a2k Hybrid Inhibitors of Malarial Dihydrofolate Reductase with Dual Binding Modes That Can Forestall Resistance.
Resolution2.38 Å
Binding residue
(original residue number in PDB)
C490 H491 Q509 R510 S511 D513 G517 N521 H551 Y553
Binding residue
(residue number reindexed from 1)
C409 H410 Q428 R429 S430 D432 G436 N440 H470 Y472
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) L36 D44 E301 W323 Y349 C409 R429 D432
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:6a2k, PDBe:6a2k, PDBj:6a2k
PDBsum6a2k
PubMed30613332
UniProtA7UD81

[Back to BioLiP]