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Structure of PDB 2yof Chain B Binding Site BS01

Receptor Information

>2yof Chain B (length=204) Species: 36329 (Plasmodium falciparum 3D7)

MTDDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETG
IGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRY
AYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQEEIYEKV
ETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFN
FLWS

Ligand information

• Ligand ID: 74W
• InChI: InChI=1S/C18H18ClF3N4O4S/c1-8-7-26(17(29)25-15(8)28)14-5-12(27)13(30-14)6-23-16(31)24-9-2-3-11(19)10(4-9)18(20,21)22/h2-4,7,12-14,27H,5-6H2,1H3,(H2,23,24,31)(H,25,28,29)/t12-,13+,14+/m0/s1
• InChIKey: IJDGQXGQAWBJEG-BFHYXJOUSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CNC(=S)Nc3ccc(c(c3)C(F)(F)F)Cl)O
  CACTVS 3.385: CC1=CN([CH]2C[CH](O)[CH](CNC(=S)Nc3ccc(Cl)c(c3)C(F)(F)F)O2)C(=O)NC1=O
  OpenEye OEToolkits 1.9.2: CC1=CN(C(=O)NC1=O)C2CC(C(O2)CNC(=S)Nc3ccc(c(c3)C(F)(F)F)Cl)O
  ACDLabs 12.01: FC(F)(F)c1cc(ccc1Cl)NC(=S)NCC3OC(N2C(=O)NC(=O)C(=C2)C)CC3O
  CACTVS 3.385: CC1=CN([C@H]2C[C@H](O)[C@@H](CNC(=S)Nc3ccc(Cl)c(c3)C(F)(F)F)O2)C(=O)NC1=O
• Formula: C18 H18 Cl F3 N4 O4 S
• Name: 1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-[[(2R,3S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl]thiourea;
  (THIO)UREA-BETA-DEOXYTHYMIDINE DERIVATIVE
• ChEMBL: CHEMBL1928432
• ZINC: ZINC000073198744
• PDB chain: 2yof Chain B Residue 211

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2yof Synthesis and Evaluation of Alpha-Thymidine Analogues as Novel Antimalarials.
• Resolution: 1.82 Å
• Binding residue (original residue number in PDB): D17 F44 R47 L59 F74 R78 R99 G104 Y107 E151 E154
• Binding residue (residue number reindexed from 1): D17 F44 R47 L59 F74 R78 R99 G104 Y107 E145 E148
• Annotation score: 1
• Binding affinity: MOAD: Ki=25uM
  BindingDB: Ki=25000nM

Enzymatic activity

• Enzyme Commision number: 2.7.4.8: guanylate kinase.
  2.7.4.9: dTMP kinase.

Gene Ontology

Molecular Function

• GO:0004385 guanylate kinase activity
• GO:0004550 nucleoside diphosphate kinase activity
• GO:0004798 thymidylate kinase activity
• GO:0005524 ATP binding
• GO:0016301 kinase activity
• GO:0050316 T2-induced deoxynucleotide kinase activity

Biological Process

• GO:0006177 GMP biosynthetic process
• GO:0006227 dUDP biosynthetic process
• GO:0006233 dTDP biosynthetic process
• GO:0006235 dTTP biosynthetic process
• GO:0009165 nucleotide biosynthetic process
• GO:0016310 phosphorylation
• GO:0046710 GDP metabolic process
• GO:0046940 nucleoside monophosphate phosphorylation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion

External links

• PDB: RCSB:2yof, PDBe:2yof, PDBj:2yof
• PDBsum: 2yof
• PubMed: 23240776
• UniProt: Q8I4S1|KTHY_PLAF7 Thymidylate kinase (Gene Name=TMK)

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