Structure of PDB 5kaj Chain C Binding Site BS01

Receptor Information
>5kaj Chain C (length=416) 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
DAYFSLPCAKEGIIPGAANLRLGRFAGPRVSRQVILEGRRIWAKEPEARL
LVDEVVEPDELDAAIERSLTRLDGDAVLANRRMLNLADESPDGFRAYMAE
FALMQALRLYGHDVID
Ligand information
Ligand IDYE2
InChIInChI=1S/C29H42N7O19P3S/c1-29(2,24(42)27(43)32-4-3-19(39)31-5-6-59-20(40)9-15-7-16(37)10-17(38)8-15)12-52-58(49,50)55-57(47,48)51-11-18-23(54-56(44,45)46)22(41)28(53-18)36-14-35-21-25(30)33-13-34-26(21)36/h7-10,13-14,18,22-24,28,37-38,40-42H,3-6,11-12H2,1-2H3,(H,31,39)(H,32,43)(H,47,48)(H,49,50)(H2,30,33,34)(H2,44,45,46)/b20-9+/t18-,22-,23-,24+,28-/m1/s1
InChIKeyLMMCTIXJVGWLEK-NUSWKBOXSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(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)NCCS\C(O)=C\c4cc(O)cc(O)c4
OpenEye OEToolkits 2.0.5CC(C)(COP(=O)(O)OP(=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)NCCS/C(=C/c4cc(cc(c4)O)O)/O)O
CACTVS 3.385CC(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)NCCSC(O)=Cc4cc(O)cc(O)c4
OpenEye OEToolkits 2.0.5CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=Cc4cc(cc(c4)O)O)O)O
FormulaC29 H42 N7 O19 P3 S
Name[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[(~{E})-2-[3,5-bis(oxidanyl)phenyl]-1-oxidanyl-ethenyl]sulfanylethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain5kaj Chain C 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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PDB5kaj Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase.
Resolution2.681 Å
Binding residue
(original residue number in PDB)
A188 E189 H222 R224 Y225 A233 G234 I235 N236 L237 F250 L251 R254 I294 G295 G296 Q299 P318 C319 I324 I325 G327
Binding residue
(residue number reindexed from 1)
A177 E178 H211 R213 Y214 A222 G223 I224 N225 L226 F239 L240 R243 I283 G284 G285 Q288 P307 C308 I313 I314 G316
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) I235 G296 Q299 C319
Catalytic site (residue number reindexed from 1) I224 G285 Q288 C308
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:5kaj, PDBe:5kaj, PDBj:5kaj
PDBsum5kaj
PubMed28695857
UniProtQ8KLK7|DPGC_STRTO (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase (Gene Name=BU52_01220)

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