Structure of PDB 4zyj Chain B Binding Site BS01

Receptor Information
>4zyj Chain B (length=380) Species: 1950 (Streptomyces peucetius) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLADNGLCEPKTPAGRRLLDLLERYLPALEAESRDNDREATLPVHLFDRM
RKEGVLGATVPEDLGGLGVHSLHDVALALARIAGRDAGVALALHMQFSRG
LTLDFEWRHGAPSTRPLAEDLLRQMGAGEAVICGAVKDVRGTTVLTYRLN
GRKTLVSMAGIATHYVVSTRLEERLAAPVVARTTPGLTVLDNWDGMGMRS
SGSVDIVFDGCPVDRDRVLPRGEPDDAALAGQTVSSIAMLGIYVGIAEAA
RRIALTELRRRGGAPAGVRTTVAEIDARLFALHTAVASALTTADRLADDL
SGDLAARGRAMMTPFQYAKLLVNRHSVGVVDDCLMLVGGAGYSNSHPLAR
LYRDVRAGGFMHPYNFTDGVDYLSEVALGR
Ligand information
Ligand IDTYD
InChIInChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyUJLXYODCHAELLY-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H16 N2 O11 P2
NameTHYMIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL259724
DrugBankDB03103
ZINCZINC000008215882
PDB chain4zyj Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4zyj Structure of DnmZ, a nitrososynthase in the Streptomyces peucetius anthracycline biosynthetic pathway.
Resolution2.736 Å
Binding residue
(original residue number in PDB)		T113 F116 E117 R243 G244 G256 V259 R332
Binding residue
(residue number reindexed from 1)		T102 F105 E106 R221 G222 G231 V234 R307
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) S260 E400
Catalytic site (residue number reindexed from 1) S235 E375
Enzyme Commision number 1.14.13.-
Gene Ontology
Molecular Function
GO:0003995 acyl-CoA dehydrogenase activity
GO:0004497 monooxygenase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4zyj, PDBe:4zyj, PDBj:4zyj
PDBsum4zyj
PubMed26457508
UniProtA0A0R4I990|NITSS_STRPE Amino sugar nitrososynthase DnmZ (Gene Name=dnmZ)

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