Structure of PDB 7d4n Chain A Binding Site BS02

Receptor Information
>7d4n Chain A (length=442) Species: 439493 (Candidatus Pelagibacter sp. HTCC7211) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSKVAIIGAGPCGLSILRAFEHLEKKGEKIPEIVCFEKQESWGGLWNYNW
RTGSDQYGDPVPNSMYRYLWSNGPKECLEFADYSFDQHFGKSIPSFPPRE
VLQDYILGRVSKGNIKNKIKFNTRVINTVYRNDKFEINYQDKVNDKTLSD
TFDYLVVSTGHFSVPFIPEYEGMSSFPGRIMHSHDFRDAEEFRGKNVIVL
GSSYSAEDVALQCNKYGAKSVTIGYRHNPMGFKWPKGMKEVHYLDKLDGK
KAIFKDGTEQDADVVILCTGYLHHFPFLDESLKLKTHNRLYPPKLYKGVV
WQDNHKLLYLGMQDQFHTFNMFDCQAWFARDVIMDKIKMPSDDEIDKDIN
KWVSMEEKLENPDQMIDFQTEYTKELHNISDYPKIDFELIRKHFKEWEHH
KVEDILTYRNKSFSSPVTGSVAPVHHTPWEKAMDDSMKTFLN
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 chain7d4n Chain A Residue 502 [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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PDB7d4n Structural and Mechanistic Insights Into Dimethylsulfoxide Formation Through Dimethylsulfide Oxidation.
Resolution1.999 Å
Binding residue
(original residue number in PDB)		I7 G8 G10 P11 C12 F36 E37 K38 Q39 G44 L45 W46 M65 S71 N72 V125 T159 F162 F277 Q315 T318
Binding residue
(residue number reindexed from 1)		I7 G8 G10 P11 C12 F36 E37 K38 Q39 G44 L45 W46 M65 S71 N72 V125 T159 F162 F277 Q315 T318
Annotation score2
Enzymatic activity
Enzyme Commision number 1.14.13.148: trimethylamine monooxygenase.
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0004499 N,N-dimethylaniline monooxygenase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0050661 NADP binding

View graph for
Molecular Function
External links
PDB RCSB:7d4n, PDBe:7d4n, PDBj:7d4n
PDBsum7d4n
PubMed34630359
UniProtB6BQB2|TMM_PELS7 Trimethylamine monooxygenase (Gene Name=tmm)

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