Structure of PDB 3b04 Chain C Binding Site BS01

Receptor Information
>3b04 Chain C (length=362) Species: 2286 (Saccharolobus shibatae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NRKVEHVEIAAFENVDGLSSSTFLNDVILVHQGFPGISFSEINTKTKFFR
KEISVPVMVTGMTGGRNELGRINKIIAEVAEKFGIPMGVGSQRVAIEKAE
ARESFAIVRKVAPTIPIIANLGMPQLVKGYGLKEFQDAIQMIEADAIAVH
LNPAQEVFQPEGEPEYQIYALEKLRDISKELSVPIIVKESGNGISMETAK
LLYSYGIKNFDTSGQGGTNWIAIEMIRDIRRGNWKAESAKNFLDWGVPTA
ASIMEVRYSVPDSFLVGSGGIRSGLDAAKAIALGADIAGMALPVLKSAIE
GKESLEQFFRKIIFELKAAMMLTGSKDVDALKKTSIVILGKLKEWAEYRG
INLSIYEKVRKR
Ligand information
Ligand IDOOP
InChIInChI=1S/C23H35N4O17P3/c1-11(4-5-42-47(40,41)44-46(37,38)39)14(9-28)23-20(24-22(33)25-21(23)32)27(16-7-13(3)12(2)6-15(16)26-23)8-17(29)19(31)18(30)10-43-45(34,35)36/h6-7,14,17-19,26,28-31H,1,4-5,8-10H2,2-3H3,(H,40,41)(H,25,32,33)(H2,34,35,36)(H2,37,38,39)/t14-,17+,18-,19+,23-/m1/s1
InChIKeyKSKIGIXASYOSHG-TUUFUFLPSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Cc1cc2N[C@@]3([C@H](CO)C(=C)CCO[P](O)(=O)O[P](O)(O)=O)C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
OpenEye OEToolkits 1.7.2Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3(N2)C(CO)C(=C)CCOP(=O)(O)OP(=O)(O)O)CC(C(C(COP(=O)(O)O)O)O)O
ACDLabs 12.01O=P(O)(O)OCC(O)C(O)C(O)CN2C3=NC(=O)NC(=O)C3(Nc1cc(c(cc12)C)C)C(C(=C)/CCOP(=O)(O)OP(=O)(O)O)CO
OpenEye OEToolkits 1.7.2Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)[C@@]3(N2)[C@H](CO)C(=C)CCO[P@](=O)(O)OP(=O)(O)O)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
CACTVS 3.370Cc1cc2N[C]3([CH](CO)C(=C)CCO[P](O)(=O)O[P](O)(O)=O)C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
FormulaC23 H35 N4 O17 P3
Name1-deoxy-1-[(4aR)-4a-[(2R)-1-hydroxy-5-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-3-methylidenepentan-2-yl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol
ChEMBL
DrugBank
ZINCZINC000098209268
PDB chain3b04 Chain C 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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PDB3b04 Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		R7 K8 A15 T65 G66 M67 G95 S96 R98 N125 H155 Q160 K193 S218 G222 T223 W225 G274 R277 A296 L297
Binding residue
(residue number reindexed from 1)		R2 K3 A10 T60 G61 M62 G90 S91 R93 N120 H150 Q155 K188 S213 G217 T218 W220 G269 R272 A291 L292
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:3b04, PDBe:3b04, PDBj:3b04
PDBsum3b04
PubMed22158896
UniProtP61615|IDI2_SACSH Isopentenyl-diphosphate delta-isomerase (Gene Name=fni)

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