Structure of PDB 6fd2 Chain B Binding Site BS01

Receptor Information
>6fd2 Chain B (length=453) Species: 1933 (Streptoalloteichus tenebrarius) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLGTVLLVSPKTSFGRDLQRTYAGGLGTVCKDEDFLLPPLDLMRLAGVLR
EDADDIAIADEEVTGVVPSVEPGTTVICHVSLPSLLEDAERLATFRAQGA
RCYAYTSIRSPAQWRTLFERGGCEGVLLPESISFARAALAGDHTVPGLVT
PDSLLDPRHHQPAFGDLAAEPLPARDLVDHTPYMFPPIARTGITSINGSF
GCPYPCRFYCPYPLSEGRKIRTYPVERIVAEFRQCAELGITAAVFRDPVF
SFHRDRTLELCQALKAADTGVPWWCETRIDRLDEEVVAALVDAGCVGVEV
GVESGDPDMQATAVRKRLNLDTVRKFHAVARKAGLKLVFLFLIGLPRETR
MSIRRTFDFILELGLADTEFNLSVITPYPGTELHQIAVDKGWIDGSQNAF
TSHNAVMHTDELSIGDLERASRFVDELHAVCKAGPAERAEFQARVHAWST
GDA
Ligand information
Ligand IDD5E
InChIInChI=1S/C12H25N3O7/c13-3-1-4(14)11(10(20)7(3)17)22-12-6(15)9(19)8(18)5(2-16)21-12/h3-12,16-20H,1-2,13-15H2/t3-,4+,5-,6-,7+,8-,9-,10-,11-,12-/m1/s1
InChIKeyJGSMDVGTXBPWIM-HKEUSBCWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)N)O)O)N
CACTVS 3.385N[CH]1C[CH](N)[CH](O[CH]2O[CH](CO)[CH](O)[CH](O)[CH]2N)[CH](O)[CH]1O
OpenEye OEToolkits 2.0.6C1C(C(C(C(C1N)OC2C(C(C(C(O2)CO)O)O)N)O)O)N
CACTVS 3.385N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2N)[C@H](O)[C@H]1O
FormulaC12 H25 N3 O7
Nameparomamine
ChEMBLCHEMBL606552
DrugBank
ZINC
PDB chain6fd2 Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6fd2 1,2-Diol Dehydration by the Radical SAM Enzyme AprD4: A Matter of Proton Circulation and Substrate Flexibility.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		Y26 A27 E37 F39 Y216 E280 E303 N375 S377
Binding residue
(residue number reindexed from 1)		Y22 A23 E33 F35 Y212 E276 E299 N371 S373
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:6fd2, PDBe:6fd2, PDBj:6fd2
PDBsum6fd2
PubMed29300094
UniProtQ2MFI7

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