Structure of PDB 2np9 Chain C Binding Site BS01

Receptor Information
>2np9 Chain C (length=421) 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
DAYFSLPAAKEGIIPGAANLRLGRFAGPRVSRQVILEGRRIWAKEPEARL
LVDEVVEPDELDAAIERSLTRLDGDAVLANRRMLNLADESPDGFRAYMAE
FALMQALRLYGHDVIDKVGRF
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 chain2np9 Chain C Residue 999 [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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PDB2np9 Structural basis for cofactor-independent dioxygenation in vancomycin biosynthesis.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		L186 A188 E189 H222 Y225 A233 G234 I235 K238 F250 L251 R254 G296 Q299 I324 I325 G327 F432
Binding residue
(residue number reindexed from 1)		L175 A177 E178 H211 Y214 A222 G223 I224 K227 F239 L240 R243 G285 Q288 I313 I314 G316 F421
Annotation score3
Binding affinityMOAD: Ki=2.7uM
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:2np9, PDBe:2np9, PDBj:2np9
PDBsum2np9
PubMed17507985
UniProtQ8KLK7|DPGC_STRTO (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase (Gene Name=BU52_01220)

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