Structure of PDB 7d9j Chain A Binding Site BS01

Receptor Information
>7d9j Chain A (length=577) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YYPPALTGLRGSHPGAFEVAHQMGWEKKTFDVDHLPIEEEYDLVVVGGGI
SGLAAAWFYRERHPAARILVIENHDDFGGHAKRNEFQAGGRTILGYGGSE
SLQSPNALYSEDAKHLLKRLGVELKRFETAFDTDFYPGLGLSRAVFFDKA
SFGVDKLVSGDPTPMVADEVPRDRLNARSWRAFIGDFPLSREDREALIAL
YESPRDYLAGKSVEEKETYLAKTSYRDYLLKNVGLSETSVKYFQGRSNDF
SALGADALPAADAYAAGFPGFDALGLPQDEPYIYHFPDGNASLARLMVRD
LIPAVAPGRGMEDIVMARFDYSKLDLAGHPVRLRLNSTAVSVRNRAGGVD
VGYSRAGRLHRVRGKHCVMACYNMMVPYLLRDLSEEQAHALSQNVKFPLV
ATKVLLRNWQAWKTLGIHEIYAPTLPYSRIKLDFPVDLGSYRHPRDPRQP
IGVHMVYVPTTPNAGMDARTQARVGRSKLYAMSFEQLEKDIRDQLQAMLG
PAGFDHRRDITGITVNRWSHGYSYFMNTLYDDEAESEALMELARSKVGNV
AIANSDAAWDAYAHAAIDQAVRAVREL
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 chain7d9j 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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PDB7d9j Structure of Pseudomonas aeruginosa spermidine dehydrogenase: a polyamine oxidase with a novel heme-binding fold.
Resolution2.19 Å
Binding residue
(original residue number in PDB)		G80 G82 S84 E105 N106 H107 G112 H113 G131 S132 E133 S134 A381 C413 Y414 M417 Y564 N596 S597 A603 Y604 A605 A608
Binding residue
(residue number reindexed from 1)		G47 G49 S51 E72 N73 H74 G79 H80 G98 S99 E100 S101 A339 C371 Y372 M375 Y522 N554 S555 A561 Y562 A563 A566
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:7d9j, PDBe:7d9j, PDBj:7d9j
PDBsum7d9j
PubMed34741591
UniProtQ9HXS8

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