Structure of PDB 5mog Chain C Binding Site BS01

Receptor Information
>5mog Chain C (length=470) Species: 39946 (Oryza sativa Indica Group) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKPLQVVIAGAGLAGLSTAKYLADAGHKPILLEARDVLGGKIAAWKDEDG
DWYETGLHIFFGAYPNIQNLFGELGINDRLQWKEHSMIFAMPNKPGEFSR
FDFPETLPAPLNGIWAILRNNEMLTWPEKVKFALGLLPAMVGGQAYVEAQ
DGFTVSEWMKKQGVPDRVNDEVFIAMSKALNFINPDELSMQCILIALNRF
LQEKHGSKMAFLDGNPPERLCMPIVDHVRSLGGEVRLNSRIQKIELNPDG
TVKHFALTDGTQITGDAYVFATPVDILKLLVPQEWKEISYFKKLEKLVGV
PVINVHIWFDRKLKNTYDHLLFSRSSLLSVYADMSVTCKEYYDPNRSMLE
LVFAPAEEWVGRSDTEIIEATMQELAKLFPDEIAADQSKAKILKYHVVKT
PRSVYKTIPDCEPCRPLQRSPIEGFYLAGDYTKQKYLASMEGAVLSGKLC
AQSVVEDYKMLSRRSLKSLQ
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain5mog Chain C Residue 600 [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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PDB5mog Structure of Phytoene Desaturase Provides Insights into Herbicide Binding and Reaction Mechanisms Involved in Carotene Desaturation.
Resolution2.77 Å
Binding residue
(original residue number in PDB)		G111 G113 A115 E134 A135 G141 K142 I143 G157 L158 H159 I160 Y165 F283 R341 I342 T373 V403 G530 D531 S540 M541 A544
Binding residue
(residue number reindexed from 1)		G10 G12 A14 E33 A34 G40 K41 I42 G56 L57 H58 I59 Y64 F182 R240 I241 T272 V302 G429 D430 S439 M440 A443
Annotation score1
Enzymatic activity
Enzyme Commision number 1.3.5.5: 15-cis-phytoene desaturase.
Gene Ontology
Molecular Function
GO:0016166 phytoene dehydrogenase activity
GO:0016491 oxidoreductase activity
Biological Process
GO:0016117 carotenoid biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5mog, PDBe:5mog, PDBj:5mog
PDBsum5mog
PubMed28669634
UniProtA2XDA1|PDS_ORYSI 15-cis-phytoene desaturase, chloroplastic/chromoplastic (Gene Name=PDS1)

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