Structure of PDB 5kah Chain J Binding Site BS01

Receptor Information
>5kah Chain J (length=419) Species: 55952 (Streptomyces toyocaensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DGLWAALTEAAASVEKLLATLPEHGARSSAERAEIAAAHDAARALRVRFL
DTHADAVYDRLTDHRRVHLRLAELVEAAATAFPGLVPTQQQLAVERSLPQ
AAKEGHEIDQGIFLRAVLRSPLAGPHLLDAMLRPTPRALELLPEFVRTGE
VEMEAVHLERRDGVARLTMCRDDRLNAEDGQQVDDMETAVDLALLDPGVR
VGLLRGGVMSHPRYRGKRVFSAGINLKYLSQGGISLVDFLMRRELGYIHK
LVRGVLTNDDRPGWWHSPRIEKPWVAAVDGFAIGGGAQLLLVFDRVLASS
DAYFSLPAGIIPGAANLRLGRFAGPRVSRQVILEGRRIWAKEPEARLLVD
EVVEPDELDAAIERSLTRLDGDAVLANRRMLNLADESPDGFRAYMAEFAL
MQALRLYGHDTIDKVGRFG
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 chain5kah Chain J Residue 501 [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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PDB5kah Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase.
Resolution2.779 Å
Binding residue
(original residue number in PDB)		L186 A188 E189 H222 R224 Y225 A233 G234 I235 N236 L237 K238 L251 R254 F292 G295 G296 P318 I324 I325 G327 F432
Binding residue
(residue number reindexed from 1)		L175 A177 E178 H211 R213 Y214 A222 G223 I224 N225 L226 K227 L240 R243 F281 G284 G285 P307 I310 I311 G313 F418
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) I235 G296 Q299 A319
Catalytic site (residue number reindexed from 1) I224 G285 Q288 A308
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:5kah, PDBe:5kah, PDBj:5kah
PDBsum5kah
PubMed28695857
UniProtQ8KLK7|DPGC_STRTO (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase (Gene Name=BU52_01220)

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