Structure of PDB 2amt Chain A Binding Site BS02

Receptor Information
>2amt Chain A (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 A Residue 1901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		H34 D56 I57 G58 F61 P62
Binding residue
(residue number reindexed from 1)		H34 D56 I57 G58 F61 P62
Annotation score2
Binding affinityMOAD: Kd=36uM
PDBbind-CN: -logKd/Ki=4.44,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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