Structure of PDB 3b03 Chain D Binding Site BS01

Receptor Information
>3b03 Chain D (length=364) Species: 2286 (Saccharolobus shibatae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVNRKVEHVEIAAFENVDGLSSSTFLNDVILVHQGFPGISFSEINTKTKF
FRKEISVPVMVTGMTGGRNELGRINKIIAEVAEKFGIPMGVGSQRVAIEK
AEARESFAIVRKVAPTIPIIANLGMPQLVKGYGLKEFQDAIQMIEADAIA
VHLNPAQEVFQPEGEPEYQIYALEKLRDISKELSVPIIVKESGNGISMET
AKLLYSYGIKNFDTSGQGGTNWIAIEMIRDIRRGNWKAESAKNFLDWGVP
TAASIMEVRYSVPDSFLVGSGGIRSGLDAAKAIALGADIAGMALPVLKSA
IEGKESLEQFFRKIIFELKAAMMLTGSKDVDALKKTSIVILGKLKEWAEY
RGINLSIYEKVRKR
Ligand information
Ligand IDVNR
InChIInChI=1S/C23H35N4O16P3/c1-4-14(5-6-41-46(39,40)43-45(36,37)38)9-23-20(24-22(32)25-21(23)31)27(16-8-13(3)12(2)7-15(16)26-23)10-17(28)19(30)18(29)11-42-44(33,34)35/h4,7-8,17-19,26,28-30H,5-6,9-11H2,1-3H3,(H,39,40)(H,25,31,32)(H2,33,34,35)(H2,36,37,38)/b14-4+/t17-,18+,19-,23+/m0/s1
InChIKeyOAOWJIIZSRFUAL-QCJQWHCGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CC=C(CCOP(=O)(O)OP(=O)(O)O)CC12C(=O)NC(=O)N=C1N(c3cc(c(cc3N2)C)C)CC(C(C(COP(=O)(O)O)O)O)O
CACTVS 3.370CC=C(CCO[P](O)(=O)O[P](O)(O)=O)C[C]12Nc3cc(C)c(C)cc3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)C1=NC(=O)NC2=O
CACTVS 3.370C/C=C(CCO[P](O)(=O)O[P](O)(O)=O)/C[C@@]12Nc3cc(C)c(C)cc3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)C1=NC(=O)NC2=O
ACDLabs 12.01O=P(O)(O)OCC(O)C(O)C(O)CN2C3=NC(=O)NC(=O)C3(Nc1cc(c(cc12)C)C)CC(=C/C)/CCOP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.7.2C/C=C(\CCO[P@](=O)(O)OP(=O)(O)O)/C[C@]12C(=O)NC(=O)N=C1N(c3cc(c(cc3N2)C)C)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
FormulaC23 H35 N4 O16 P3
Name1-deoxy-1-[(4aR)-4a-[(2Z)-2-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)but-2-en-1-yl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol
ChEMBL
DrugBank
ZINCZINC000098209531
PDB chain3b03 Chain D Residue 669 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3b03 Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R7 K8 T65 G66 M67 G95 S96 R98 N125 H155 N157 Q160 K193 S195 S218 G222 T223 W225 R277 A296 L297
Binding residue
(residue number reindexed from 1)		R4 K5 T62 G63 M64 G92 S93 R95 N122 H152 N154 Q157 K190 S192 S215 G219 T220 W222 R274 A293 L294
Annotation score1
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:3b03, PDBe:3b03, PDBj:3b03
PDBsum3b03
PubMed22158896
UniProtP61615|IDI2_SACSH Isopentenyl-diphosphate delta-isomerase (Gene Name=fni)

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