Structure of PDB 2ivd Chain A Binding Site BS02

Receptor Information
>2ivd Chain A (length=449) Species: 34 (Myxococcus xanthus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNVAVVGGGISGLAVAHHLRSRGTDAVLLESSARLGGAVGTHALAGYLVE
QGPNSFLDREPATRALAAALNLEGRIRAADPAAKRRYVYTRGRLRSVPAS
PPAFLASDILPLGARLRVAGELFSRRAPEGVDESLAAFGRRHLGHRATQV
LLDAVQTGIYAGDVEQLSVAATFPMLVKMEREHRSLILGAIRAQKAQRQA
GTAPKLSGALSTFDGGLQVLIDALAASLGDAAHVGARVEGLAREGWRLII
EEHGRRAELSVAQVVLAAPAHATAKLLRPLDDALAALVAGIAYAPIAVVH
LGFDAGTLPAPDGFGFLVPAEEQRRMLGAIHASTTFPFRAEGGRVLYSCM
VGGARQPGLVEQDEDALAALAREELKALAGVTARPSFTRVFRWPLGIPQY
NLGHLERVAAIDAALQRLPGLHLIGNAYKGVGLNDCIRNAAQLADALVA
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 chain2ivd Chain A Residue 1466 [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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PDB2ivd Crystal Structure of Protoporphyrinogen Oxidase from Myxococcus Xanthus and its Complex with the Inhibitor Acifluorfen.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		V15 G16 G18 I19 S20 L38 E39 S40 G46 A47 G61 P62 S64 V251 P284 I412 G440 N441 V446 G447 L448
Binding residue
(residue number reindexed from 1)		V6 G7 G9 I10 S11 L29 E30 S31 G37 A38 G52 P53 S55 V238 P269 I397 G425 N426 V431 G432 L433
Annotation score1
Enzymatic activity
Enzyme Commision number 1.3.3.4: protoporphyrinogen oxidase.
Gene Ontology
Molecular Function
GO:0004729 oxygen-dependent protoporphyrinogen oxidase activity
GO:0016491 oxidoreductase activity
Biological Process
GO:0006779 porphyrin-containing compound biosynthetic process
GO:0006782 protoporphyrinogen IX biosynthetic process
GO:0006783 heme biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2ivd, PDBe:2ivd, PDBj:2ivd
PDBsum2ivd
PubMed17046834
UniProtP56601|PGOX_MYXXA Protoporphyrinogen oxidase (Gene Name=pgoX)

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