Structure of PDB 7d4m Chain B Binding Site BS01

Receptor Information
>7d4m Chain B (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 IDNAP
InChIInChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain7d4m Chain B Residue 501 [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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PDB7d4m Structural and Mechanistic Insights Into Dimethylsulfoxide Formation Through Dimethylsulfide Oxidation.
Resolution1.786 Å
Binding residue
(original residue number in PDB)		W70 N72 F162 P168 Y170 S202 S203 Y204 S205 D208 R226 H227 C268 T269 G270
Binding residue
(residue number reindexed from 1)		W70 N72 F162 P168 Y170 S202 S203 Y204 S205 D208 R226 H227 C268 T269 G270
Annotation score4
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:7d4m, PDBe:7d4m, PDBj:7d4m
PDBsum7d4m
PubMed34630359
UniProtB6BQB2|TMM_PELS7 Trimethylamine monooxygenase (Gene Name=tmm)

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