Structure of PDB 5iwy Chain B Binding Site BS01

Receptor Information
>5iwy Chain B (length=158) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MFRIGQGFDVHQLVEGRPLIIGGIEIPYEKGLLGHSDADVLLHTVADACL
GAVGEGDIGKHFPDTDPEFKDADSFKLLQHVWGIVKQKGYVLGNIDCTII
AQKPKMLPYIEDMRKRIAEGLEADVSQVNVKATTTEKLGFTGRAEGIAAQ
ATVLIQKG
Ligand information
Ligand IDC5P
InChIInChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyIERHLVCPSMICTF-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H14 N3 O8 P
NameCYTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL307679
DrugBankDB03403
ZINCZINC000003861744
PDB chain5iwy Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5iwy Crystal structure of IspF from Bacillus subtilis and absence of protein complex assembly among IspD/IspE/IspF enzymes in the MEP pathway.
Resolution1.99 Å
Binding residue
(original residue number in PDB)		K105 M106 L107 A132 T133 T134
Binding residue
(residue number reindexed from 1)		K105 M106 L107 A132 T133 T134
Annotation score3
Enzymatic activity
Enzyme Commision number 4.6.1.12: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase.
Gene Ontology
Molecular Function
GO:0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
GO:0016829 lyase activity
GO:0046872 metal ion binding
Biological 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:5iwy, PDBe:5iwy, PDBj:5iwy
PDBsum5iwy
PubMed29335298
UniProtQ06756|ISPF_BACSU 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (Gene Name=ispF)

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