Structure of PDB 2d5n Chain B Binding Site BS02

Receptor Information
>2d5n Chain B (length=359) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHA
EVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMR
DPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTL
KAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADN
PSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEE
KKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFV
KEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGR
DIKLTAKPT
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain2d5n Chain B Residue 381 [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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PDB2d5n Crystal structure of a bifunctional deaminase and reductase involved in riboflavin biosynthesis
Resolution2.97 Å
Binding residue
(original residue number in PDB)		A152 A153 I160 G192 G194 T195 T221 I270 E290 G292 S293 A294 V295 S298
Binding residue
(residue number reindexed from 1)		A152 A153 I160 G192 G194 T195 T221 I270 E290 G292 S293 A294 V295 S298
Annotation score4
Enzymatic activity
Enzyme Commision number 1.1.1.193: 5-amino-6-(5-phosphoribosylamino)uracil reductase.
3.5.4.26: diaminohydroxyphosphoribosylaminopyrimidine deaminase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008270 zinc ion binding
GO:0008703 5-amino-6-(5-phosphoribosylamino)uracil reductase activity
GO:0008835 diaminohydroxyphosphoribosylaminopyrimidine deaminase activity
GO:0016491 oxidoreductase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0050661 NADP binding
Biological Process
GO:0009231 riboflavin biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2d5n, PDBe:2d5n, PDBj:2d5n
PDBsum2d5n
PubMed
UniProtP17618|RIBD_BACSU Riboflavin biosynthesis protein RibD (Gene Name=ribD)

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