Structure of PDB 7d9h Chain A Binding Site BS01

Receptor Information
>7d9h Chain A (length=572) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YYPPALTGLRGSHPGAFEVAHQMGWEKKTFDVDHLPIEEEYDLVVVGGGI
SGLAAAWFYRERHPAARILVIENHDDFGGHAKRNEFQAGGRTILGYGGSE
SLQSYSEDAKHLLKRLGVELKRFETAFDTDFYPGLGLSRAVFFDKASFGV
DKLVSGDPTPMVADEVPRDRLNARSWRAFIGDFPLSREDREALIALYESP
RDYLAGKSVEEKETYLAKTSYRDYLLKNVGLSETSVKYFQGRSNDFSALG
ADALPAADAYAAGFPGFDALGLPDEPYIYHFPDGNASLARLMVRDLIPAV
APGRGMEDIVMARFDYSKLDLAGHPVRLRLNSTAVSVRNRAGGVDVGYSR
AGRLHRVRGKHCVMACYNMMVPYLLRDLSEEQAHALSQNVKFPLVYTKVL
LRNWQAWKTLGIHEIYAPTLPYSRIKLDFPVDLGSYRHPRDPRQPIGVHM
VYVPTTPNAGMDARTQARVGRSKLYAMSFEQLEKDIRDQLQAMLGPAGFD
HRRDITGITVNRWSHGYSYFMNTLYDDEAESEALMELARSKVGNVAIANS
DAAWDAYAHAAIDQAVRAVREL
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 chain7d9h Chain A Residue 701 [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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PDB7d9h Structure of Pseudomonas aeruginosa spermidine dehydrogenase: a polyamine oxidase with a novel heme-binding fold.
Resolution2.31 Å
Binding residue
(original residue number in PDB)		G80 G82 S84 E105 N106 H107 G112 H113 G131 S132 E133 S134 A381 C413 Y414 M417 Y443 G563 Y564 N596 S597 A603 Y604 A605
Binding residue
(residue number reindexed from 1)		G47 G49 S51 E72 N73 H74 G79 H80 G98 S99 E100 S101 A334 C366 Y367 M370 Y396 G516 Y517 N549 S550 A556 Y557 A558
Annotation score1
Enzymatic activity
Enzyme Commision number 1.5.99.6: spermidine dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:7d9h, PDBe:7d9h, PDBj:7d9h
PDBsum7d9h
PubMed34741591
UniProtQ9HXS8

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