Structure of PDB 2yoh Chain B Binding Site BS01

Receptor Information
>2yoh Chain B (length=199) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIG
QIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAY
SGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAIYEKVETQKK
IYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS
Ligand information
Ligand IDWMJ
InChIInChI=1S/C17H19N5O7/c1-9-8-21(17(26)20-15(9)24)14-6-12(23)13(29-14)7-18-16(25)19-10-2-4-11(5-3-10)22(27)28/h2-5,8,12-14,23H,6-7H2,1H3,(H2,18,19,25)(H,20,24,26)/t12-,13+,14-/m0/s1
InChIKeyGGXGAHUHZPSFRR-MJBXVCDLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CC1=CN(C(=O)NC1=O)[C@@H]2C[C@@H]([C@H](O2)CNC(=O)Nc3ccc(cc3)[N+](=O)[O-])O
CACTVS 3.385CC1=CN([C@@H]2C[C@H](O)[C@@H](CNC(=O)Nc3ccc(cc3)[N+]([O-])=O)O2)C(=O)NC1=O
CACTVS 3.385CC1=CN([CH]2C[CH](O)[CH](CNC(=O)Nc3ccc(cc3)[N+]([O-])=O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.9.2CC1=CN(C(=O)NC1=O)C2CC(C(O2)CNC(=O)Nc3ccc(cc3)[N+](=O)[O-])O
ACDLabs 12.01[O-][N+](=O)c1ccc(cc1)NC(=O)NCC3OC(N2C(=O)NC(=O)C(=C2)C)CC3O
FormulaC17 H19 N5 O7
Name1-[[(2R,3S,5S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl]-3-(4-nitrophenyl)urea
ChEMBLCHEMBL2178479
DrugBank
ZINCZINC000095578670
PDB chain2yoh Chain B Residue 211 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yoh Synthesis and Evaluation of Alpha-Thymidine Analogues as Novel Antimalarials.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		F44 P45 L59 K60 F74 R78 R99 S103 G104 Y107
Binding residue
(residue number reindexed from 1)		F42 P43 L57 K58 F72 R76 R97 S101 G102 Y105
Annotation score2
Binding affinityMOAD: Ki=11uM
BindingDB: Ki=11000nM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2yoh, PDBe:2yoh, PDBj:2yoh
PDBsum2yoh
PubMed23240776
UniProtQ8I4S1|KTHY_PLAF7 Thymidylate kinase (Gene Name=TMK)

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