Structure of PDB 7d9g Chain B Binding Site BS01

Receptor Information
>7d9g Chain B (length=588) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRYYPPALTGLRGSHPGAFEVAHQMGWEKKTFDVDHLPIEEEYDLVVVGG
GISGLAAAWFYRERHPAARILVIENHDDFGGHAKRNEFQAGGRTILGYGG
SESLQSPNALYSEDAKHLLKRLGVELKRFETAFDTDFYPGLGLSRAVFFD
KASFGVDKLVSGDPTPMVADEVPRDRLNARSWRAFIGDFPLSREDREALI
ALYESPRDYLAGKSVEEKETYLAKTSYRDYLLKNVGLSETSVKYFQGRSN
DFSALGADALPAADAYAAGFPGFDALGLPQPSEEAQAEMDEPYIYHFPDG
NASLARLMVRDLIPAVAPGRGMEDIVMARFDYSKLDLAGHPVRLRLNSTA
VSVRNRAGGVDVGYSRAGRLHRVRGKHCVMACYNMMVPYLLRDLSEEQAH
ALSQNVKFPLVYTKVLLRNWQAWKTLGIHEIYAPTLPYSRIKLDFPVDLG
SYRHPRDPRQPIGVHMVYVPTTPNAGMDARTQARVGRSKLYAMSFEQLEK
DIRDQLQAMLGPAGFDHRRDITGITVNRWSHGYSYFMNTLYDDEAESEAL
MELARSKVGNVAIANSDAAWDAYAHAAIDQAVRAVREL
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 chain7d9g Chain B 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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PDB7d9g Structure of Pseudomonas aeruginosa spermidine dehydrogenase: a polyamine oxidase with a novel heme-binding fold.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		V79 G82 S84 E105 N106 H107 G112 H113 G131 S132 E133 S134 T380 A381 C413 Y414 M417 Y443 G563 Y564 N596 S597 A603 Y604 A605
Binding residue
(residue number reindexed from 1)		V48 G51 S53 E74 N75 H76 G81 H82 G100 S101 E102 S103 T349 A350 C382 Y383 M386 Y412 G532 Y533 N565 S566 A572 Y573 A574
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:7d9g, PDBe:7d9g, PDBj:7d9g
PDBsum7d9g
PubMed34741591
UniProtQ9HXS8

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