Structure of PDB 2zru Chain B Binding Site BS01

Receptor Information
>2zru Chain B (length=356) Species: 2286 (Saccharolobus shibatae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VEHVEIAAFENVDGLSSSTFLNDVILVHQGFPGISFSEINTKTKFFRKEI
SVPVMVTGMTNELGRINKIIAEVAEKFGIPMGVGSQRVAIEKAEARESFA
IVRKVAPTIPIIANLGMPQLVKGYGLKEFQDAIQMIEADAIAVHLNPAQE
VFQPEGEPEYQIYALEKLRDISKELSVPIIVKESGNGISMETAKLLYSYG
IKNFDTSGQGGTNWIAIEMIRDIRRGNWKAESAKNFLDWGVPTAASIMEV
RYSVPDSFLVGSGGIRSGLDAAKAIALGADIAGMALPVLKSAIEGKESLE
QFFRKIIFELKAAMMLTGSKDVDALKKTSIVILGKLKEWAEYRGINLSIY
EKVRKR
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 chain2zru Chain B Residue 669 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2zru New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		T65 G66 M67 T68 G95 S96 N125 H155 K193 S218 T223 W225 R277 M295 A296 L297
Binding residue
(residue number reindexed from 1)		T57 G58 M59 T60 G84 S85 N114 H144 K182 S207 T212 W214 R266 M284 A285 L286
Annotation score1
Binding affinityMOAD: Kd=467nM
Enzymatic activity
Enzyme Commision number 5.3.3.2: isopentenyl-diphosphate Delta-isomerase.
Gene Ontology
Molecular Function
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:2zru, PDBe:2zru, PDBj:2zru
PDBsum2zru
PubMed19158086
UniProtP61615|IDI2_SACSH Isopentenyl-diphosphate delta-isomerase (Gene Name=fni)

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