Structure of PDB 3k2h Chain B Binding Site BS02

Receptor Information
>3k2h Chain B (length=503) Species: 5865 (Babesia bovis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYEGCGDLTIFVAVALNKVIGHKNQIPWPHITHDFRFLRNGTTYIPPEVL
SKNPDIQNVVIFGRKTYESIPKASLPLKNRINVILSRTVKEVPGCLVYED
LSTAIRDLRANVPHNKIFILGGSFLYKEVLDNGLCDKIYLTRLNKEYPGD
TYFPDIPDTFEITAISPTFSTDFVSYDFVIYERKDCKPPFDQLLMTGTDI
SVPKPKYVACPGVRIRNHEEFQYLDILADVLSHGVLKPNRTGTDAYSKFG
YQMRFDLSRSFPLLTTKKVALRSIIEELLWFIKGSTNGNDLLAKNVRIWE
LNGRRDFLDKNGFTDREEHDLGPIYGFQWRHFGAEYLDMHADYTGKGIDQ
LAEIINRIKTNPNDRRLIVCSWNVSDLKKMALPPCHCFFQFYVSDNKLSC
MMHQRSCDLGLGVPFNIASYSILTAMVAQVCGLGLGEFVHNLADAHIYVD
HVDAVTTQIARIPHPFPRLRLNPDIRNIEDFTIDDIVVEDYVSHPPIPMA
MSA
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 chain3k2h Chain B Residue 512 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3k2h Inhibitor-bound complexes of dihydrofolate reductase-thymidylate synthase from Babesia bovis.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R248 C393 H394 Q412 R413 S414 C415 D416 N424 H454 Y456
Binding residue
(residue number reindexed from 1)		R240 C385 H386 Q404 R405 S406 C407 D408 N416 H446 Y448
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) I29 D37 E285 W307 Y333 C393 R413 D416
Catalytic site (residue number reindexed from 1) I26 D34 E277 W299 Y325 C385 R405 D408
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
View graph for
Cellular Component
External links
PDB RCSB:3k2h, PDBe:3k2h, PDBj:3k2h
PDBsum3k2h
PubMed21904052
UniProtA7ASX7

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