Structure of PDB 5bkc Chain A Binding Site BS03

Receptor Information
>5bkc Chain A (length=289) Species: 80866 (Delftia acidovorans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLSQRFERIAVQPLTGVLGAEITGVDLREPLDDSTWNEILDAFHTYQVIY
FPGQAITNEQHIAFSRRFGPVDPVPLLKSIEGYPEVQMIRREANESGRVI
GDDWHTDSTFLDAPPAAVVMRAIDVPEHGGDTGFLSMYTAWETLSPTMQA
TIEGLNVVHSATRVFGSLYQAQNRRFSNTSVKVMDVDAGDRETVHPLVVT
HPGSGRKGLYVNQVYCQRIEGMTDAESKPLLQFLYEHATRFDFTCRVRWK
KDQVLVWDNLCTMHRAVPDYAGKFRYLTRTTVGGVRPAR
Ligand information
Ligand IDO0D
InChIInChI=1S/C14H11Cl2NO4/c1-8(14(18)19)20-10-2-4-11(5-3-10)21-13-12(16)6-9(15)7-17-13/h2-8H,1H3,(H,18,19)/t8-/m1/s1
InChIKeySVGBNTOHFITEDI-MRVPVSSYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C(=O)O)Oc1ccc(cc1)Oc2c(cc(cn2)Cl)Cl
CACTVS 3.385C[CH](Oc1ccc(Oc2ncc(Cl)cc2Cl)cc1)C(O)=O
OpenEye OEToolkits 2.0.7C[C@H](C(=O)O)Oc1ccc(cc1)Oc2c(cc(cn2)Cl)Cl
CACTVS 3.385C[C@@H](Oc1ccc(Oc2ncc(Cl)cc2Cl)cc1)C(O)=O
ACDLabs 12.01Clc2c(Oc1ccc(cc1)OC(C)C(O)=O)ncc(c2)Cl
FormulaC14 H11 Cl2 N O4
Name(2R)-2-{4-[(3,5-dichloropyridin-2-yl)oxy]phenoxy}propanoic acid
ChEMBL
DrugBank
ZINCZINC000000139487
PDB chain5bkc Chain A Residue 503 [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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PDB5bkc Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		L83 G107 D108 D109 H111 D113 S114 F182 V220 Y221
Binding residue
(residue number reindexed from 1)		L77 G101 D102 D103 H105 D107 S108 F176 V214 Y215
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H111 D113 H270 R285
Catalytic site (residue number reindexed from 1) H105 D107 H264 R279
Enzyme Commision number 1.14.11.44: (R)-dichlorprop dioxygenase (2-oxoglutarate).
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016706 2-oxoglutarate-dependent dioxygenase activity
GO:0031418 L-ascorbic acid binding
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:5bkc, PDBe:5bkc, PDBj:5bkc
PDBsum5bkc
PubMed31209034
UniProtP83310|RDPA_DELAC (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase (Gene Name=rdpA)

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