Structure of PDB 7d9j Chain A Binding Site BS02

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 IDHEM
InChIInChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
InChIKeyKABFMIBPWCXCRK-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
ACDLabs 12.01C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O
FormulaC34 H32 Fe N4 O4
NamePROTOPORPHYRIN IX CONTAINING FE;
HEME
ChEMBL
DrugBankDB18267
ZINC
PDB chain7d9j Chain A Residue 702 [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)		S45 F50 A53 H54 W58 N106 Y414 M416 M417 Y420 R518 Y522 R559 S561 H562
Binding residue
(residue number reindexed from 1)		S12 F17 A20 H21 W25 N73 Y372 M374 M375 Y378 R476 Y480 R517 S519 H520
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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