Structure of PDB 1h48 Chain D Binding Site BS01

Receptor Information
>1h48 Chain D (length=158) Species: 511693 (Escherichia coli BL21) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LEMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDAL
LGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTI
IAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIAC
EAVALLIK
Ligand information
Ligand IDCDI
InChIInChI=1S/C5H12O9P2/c1-5(3-6)4(7)2-12-15(8,9)14-16(10,11)13-5/h4,6-7H,2-3H2,1H3,(H,8,9)(H,10,11)/t4-,5+/m1/s1
InChIKeySFRQRNJMIIUYDI-UHNVWZDZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@@]1([C@@H](CO[P@](=O)(O[P@](=O)(O1)O)O)O)CO
CACTVS 3.341C[C@@]1(CO)O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O
ACDLabs 10.04O=P1(OP(=O)(OCC(O)C(O1)(C)CO)O)O
OpenEye OEToolkits 1.5.0CC1(C(COP(=O)(OP(=O)(O1)O)O)O)CO
CACTVS 3.341C[C]1(CO)O[P](O)(=O)O[P](O)(=O)OC[CH]1O
FormulaC5 H12 O9 P2
Name2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
ChEMBL
DrugBankDB03961
ZINCZINC000008419115
PDB chain1h48 Chain D Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1h48 The Identification of Isoprenoids that Bind in the Intersubunit Cavity of Escherichia Coli 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase by Complementary Biophysical Methods
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D8 H10 H34 S35 H42 I57 G58 F61 D63
Binding residue
(residue number reindexed from 1)		D10 H12 H36 S37 H44 I59 G60 F63 D65
Annotation score5
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:1h48, PDBe:1h48, PDBj:1h48
PDBsum1h48
PubMed15608374
UniProtP62617|ISPF_ECOLI 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (Gene Name=ispF)

[Back to BioLiP]