Structure of PDB 2pg8 Chain B Binding Site BS01

Receptor Information
>2pg8 Chain B (length=417) Species: 55952 (Streptomyces toyocaensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DTDGLWAALTEAAASVEKLLATLPEHGARSSAERAEIAAAHDAARALRVR
FLDTHADAVYDRLTDHRRVHLRLAELVEAAATAFPGLVPTQQQLAVERSL
PQAAKEGHEIDQGIFLRAVLRSPLAGPHLLDAMLRPTPRALELLPEFVRT
GEVEMEAVHLERRDGVARLTMCRDDRLNAEDGQQVDDMETAVDLALLDPG
VRVGLLRGGVMSHPRYRGKRVFSAGINLKYLSQGGISLVDFLMRKELGYI
HKLVRGVLTNDDRPGWWHSPRIEKPWVAAVDGFAIGGGAQLLLVFDRVLA
SSDAYFSLPAAKEGIIPGAANLRLGRFAGPRVSRQVILEGRRIWAKEPEA
RLLVDEVVEPDELDAAIERSLTRLDGDAVLANRRMLNLADESPDGFRAYM
AEFALMQALRLYGHDVI
Ligand information
Ligand IDYE1
InChIInChI=1S/C29H43N8O19P3/c1-29(2,24(43)27(44)33-4-3-19(40)31-5-6-32-20(41)9-15-7-16(38)10-17(39)8-15)12-53-59(50,51)56-58(48,49)52-11-18-23(55-57(45,46)47)22(42)28(54-18)37-14-36-21-25(30)34-13-35-26(21)37/h7-8,10,13-14,18,22-24,28,38-39,42-43H,3-6,9,11-12H2,1-2H3,(H,31,40)(H,32,41)(H,33,44)(H,48,49)(H,50,51)(H2,30,34,35)(H2,45,46,47)/t18-,22-,23-,24+,28-/m1/s1
InChIKeyMSJGSRHUBFYIJV-CECATXLMSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCNC(=O)Cc4cc(O)cc(O)c4
ACDLabs 10.04O=C(NCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)Cc4cc(O)cc(O)c4
OpenEye OEToolkits 1.5.0CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCNC(=O)Cc4cc(cc(c4)O)O)O
CACTVS 3.341CC(C)(CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCNC(=O)Cc4cc(O)cc(O)c4
OpenEye OEToolkits 1.5.0CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCNC(=O)Cc4cc(cc(c4)O)O)O
FormulaC29 H43 N8 O19 P3
Name
ChEMBL
DrugBank
ZINCZINC000196255742
PDB chain2pg8 Chain B Residue 998 [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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PDB2pg8 Substrate Recognition and Catalysis by the Cofactor-Independent Dioxygenase DpgC.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		L186 A188 E189 H222 R224 Y225 A233 G234 I235 N236 L237 K238 L251 K254 G295 I324 I325 G327 Q416
Binding residue
(residue number reindexed from 1)		L177 A179 E180 H213 R215 Y216 A224 G225 I226 N227 L228 K229 L242 K245 G286 I315 I316 G318 Q407
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) I235 G296 Q299 A319
Catalytic site (residue number reindexed from 1) I226 G287 Q290 A310
Enzyme Commision number 1.13.11.80: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
GO:0042802 identical protein binding
Biological Process
GO:0006635 fatty acid beta-oxidation
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2pg8, PDBe:2pg8, PDBj:2pg8
PDBsum2pg8
PubMed18004875
UniProtQ8KLK7|DPGC_STRTO (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase (Gene Name=BU52_01220)

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