Structure of PDB 7d9f Chain A Binding Site BS01

Receptor Information
>7d9f Chain A (length=591) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APGGRYYPPALTGLRGSHPGAFEVAHQMGWEKKTFDVDHLPIEEEYDLVV
VGGGISGLAAAWFYRERHPAARILVIENHDDFGGHAKRNEFQAGGRTILG
YGGSESLQSPNALYSEDAKHLLKRLGVELKRFETAFDTDFYPGLGLSRAV
FFDKASFGVDKLVSGDPTPMVADEVPRDRLNARSWRAFIGDFPLSREDRE
ALIALYESPRDYLAGKSVEEKETYLAKTSYRDYLLKNVGLSETSVKYFQG
RSNDFSALGADALPAADAYAAGFPGFDALGLPQPSEEAQAEMDEPYIYHF
PDGNASLARLMVRDLIPAVAPGRGMEDIVMARFDYSKLDLAGHPVRLRLN
STAVSVRNRAGGVDVGYSRAGRLHRVRGKHCVMACYNMMVPYLLRDLSEE
QAHALSQNVKFPLVYTKVLLRNWQAWKTLGIHEIYAPTLPYSRIKLDFPV
DLGSYRHPRDPRQPIGVHMVYVPTTPNAGMDARTQARVGRSKLYAMSFEQ
LEKDIRDQLQAMLGPAGFDHRRDITGITVNRWSHGYSYFMNTLYDDEAES
EALMELARSKVGNVAIANSDAAWDAYAHAAIDQAVRAVREL
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 chain7d9f 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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PDB7d9f Structure of Pseudomonas aeruginosa spermidine dehydrogenase: a polyamine oxidase with a novel heme-binding fold.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		G80 G82 S84 E105 N106 H107 G112 H113 G131 S132 E133 S134 T380 A381 C413 Y414 M417 Y443 G563 Y564 N596 S597 A603 Y604 A605 A608
Binding residue
(residue number reindexed from 1)		G52 G54 S56 E77 N78 H79 G84 H85 G103 S104 E105 S106 T352 A353 C385 Y386 M389 Y415 G535 Y536 N568 S569 A575 Y576 A577 A580
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:7d9f, PDBe:7d9f, PDBj:7d9f
PDBsum7d9f
PubMed34741591
UniProtQ9HXS8

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