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Structure of PDB 2amt Chain C Binding Site BS03

Receptor Information
>2amt Chain C (length=156) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLG
AAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIA
QAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEA
VALLIK
Ligand information
Ligand ID1AA
InChIInChI=1S/C18H24N4O13P2/c19-11-4-2-1-3-10(11)17(25)31-7-8-32-36(27,28)35-37(29,30)33-9-12-14(23)15(24)16(34-12)22-6-5-13(20)21-18(22)26/h1-6,12,14-16,23-24H,7-9,19H2,(H,27,28)(H,29,30)(H2,20,21,26)/t12-,14-,15-,16-/m1/s1
InChIKeyPGXVRIOOHRVKLC-DTZQCDIJSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OCCOC(=O)c3ccccc3N)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1ccc(c(c1)C(=O)OCCOP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=NC3=O)N)O)O)N
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OCCOC(=O)c3ccccc3N)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1ccc(c(c1)C(=O)OCCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O)N
ACDLabs 10.04O=P(O)(OCCOC(=O)c1ccccc1N)OP(=O)(O)OCC3OC(N2C(=O)N=C(N)C=C2)C(O)C3O
FormulaC18 H24 N4 O13 P2
Name5'-O-[({[(2-{[(2-AMINOPHENYL)CARBONYL]OXY}ETHYL)OXY]PHOSPHINATO}OXY)PHOSPHINATO]CYTIDINE
ChEMBL
DrugBank
ZINCZINC000058660733
PDB chain2amt Chain C Residue 2901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2amt Fluorescent Inhibitors for IspF, an Enzyme in the Non-Mevalonate Pathway for Isoprenoid Biosynthesis and a Potential Target for Antimalarial Therapy.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		A100 K104 M105 L106 A131 T132 T133
Binding residue
(residue number reindexed from 1)		A100 K104 M105 L106 A131 T132 T133
Annotation score2
Binding affinityMOAD: Kd=36uM
Enzymatic activity
Enzyme Commision number 4.6.1.12: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
GO:0016829 lyase activity
GO:0030145 manganese ion binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006744 ubiquinone biosynthetic process
GO:0008299 isoprenoid biosynthetic process
GO:0016114 terpenoid biosynthetic process
GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2amt, PDBe:2amt, PDBj:2amt
PDBsum2amt
PubMed16392111
UniProtP62617|ISPF_ECOLI 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (Gene Name=ispF)

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