Structure of PDB 1nfs Chain A Binding Site BS03

Receptor Information
>1nfs Chain A (length=176) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRAL
SKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFR
YRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDA
TPWAFSPWMVMQATNREARKRLSAFT
Ligand information
Ligand IDDED
InChIInChI=1S/C4H13NO7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h3-4H2,1-2H3,(H,9,10)(H2,6,7,8)
InChIKeyQGKJQRINUQGSJM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CN(C)CCO[P@@](=O)(O)OP(=O)(O)O
CACTVS 3.341CN(C)CCO[P@](O)(=O)O[P](O)(O)=O
CACTVS 3.341CN(C)CCO[P](O)(=O)O[P](O)(O)=O
ACDLabs 10.04O=P(OP(=O)(OCCN(C)C)O)(O)O
OpenEye OEToolkits 1.5.0CN(C)CCOP(=O)(O)OP(=O)(O)O
FormulaC4 H13 N O7 P2
Name2-DIMETHYLAMINO-ETHYL-DIPHOSPHATE
ChEMBLCHEMBL1232165
DrugBankDB03165
ZINCZINC000012503144
PDB chain1nfs Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1nfs Catalytic Mechanism of Escherichia coli Isopentenyl Diphosphate Isomerase Involves Cys-67, Glu-116, and Tyr-104 as Suggested by Crystal Structures of Complexes with Transition State Analogues and Irreversible Inhibitors
Resolution1.96 Å
Binding residue
(original residue number in PDB)		K21 R51 C67 G68 H69 R83 Y104 E114 E116 W161
Binding residue
(residue number reindexed from 1)		K18 R48 C64 G65 H66 R80 Y101 E111 E113 W158
Annotation score2
Binding affinityMOAD: Kd<0.12nM
PDBbind-CN: -logKd/Ki=9.92,Kd<0.12nM
Enzymatic activity
Catalytic site (original residue number in PDB) H25 H32 C67 H69 E87 Y104 E114 E116 W161
Catalytic site (residue number reindexed from 1) H22 H29 C64 H66 E84 Y101 E111 E113 W158
Enzyme Commision number 5.3.3.2: isopentenyl-diphosphate Delta-isomerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004452 isopentenyl-diphosphate delta-isomerase activity
GO:0008270 zinc ion binding
GO:0016853 isomerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006974 DNA damage response
GO:0008299 isoprenoid biosynthetic process
GO:0050992 dimethylallyl diphosphate biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1nfs, PDBe:1nfs, PDBj:1nfs
PDBsum1nfs
PubMed12540835
UniProtQ46822|IDI_ECOLI Isopentenyl-diphosphate Delta-isomerase (Gene Name=idi)

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