Structure of PDB 3dh7 Chain D Binding Site BS01

Receptor Information
>3dh7 Chain D (length=313) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KHLEACLEGEVAYQKTTTGLEGFRLRYQALAGLALSEVDLTTPFLGKTLK
APFLIGAMTERINLALAEAAEALGVGMMLGSGRILLERPEAVRKVAPKAL
LIANLGLAQLRRYGRDDLLRLVEMLEADALAFHVNPLQEAVQRGDTDFRG
LVERLAELLPLPFPVMVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSW
ARVEEWVRFGEVRHPELCEIGIPTARAILEVREVLPHLPLVASGGVYTGT
DGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGA
RNPKEARGRVERV
Ligand information
Ligand IDFMN
InChIInChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
InChIKeyFVTCRASFADXXNN-SCRDCRAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
ACDLabs 12.01N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
FormulaC17 H21 N4 O9 P
NameFLAVIN MONONUCLEOTIDE;
RIBOFLAVIN MONOPHOSPHATE
ChEMBLCHEMBL1201794
DrugBankDB03247
ZINCZINC000003831425
PDB chain3dh7 Chain D Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dh7 Crystal structure of type 2 isopentenyl diphosphate isomerase from Thermus thermophilus in complex with inorganic pyrophosphate
Resolution2.97 Å
Binding residue
(original residue number in PDB)		C14 A65 M66 T67 S95 N123 H152 K187 V189 T217 W219 G263 G264 Y266 A285 R286
Binding residue
(residue number reindexed from 1)		C6 A57 M58 T59 S81 N104 H133 K168 V170 T198 W200 G244 G245 Y247 A266 R267
Annotation score1
Enzymatic activity
Enzyme Commision number 5.3.3.2: isopentenyl-diphosphate Delta-isomerase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0004452 isopentenyl-diphosphate delta-isomerase activity
GO:0010181 FMN binding
GO:0016491 oxidoreductase activity
GO:0016853 isomerase activity
GO:0046872 metal ion binding
GO:0070402 NADPH binding
Biological Process
GO:0008299 isoprenoid 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:3dh7, PDBe:3dh7, PDBj:3dh7
PDBsum3dh7
PubMed18693754
UniProtQ53W52

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