Structure of PDB 4gek Chain A Binding Site BS01

Receptor Information
>4gek Chain A (length=230) Species: 511145 (Escherichia coli str. K-12 substr. MG1655) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WTFDERVAEVFPDMIQRSVPGYSNIISMIGMLAERFVQPGTQVYDLGCSL
GAATLSVRRNIHHDNCKIIAIDNSPAMIERCRRHIDAYKAPTPVDVIEGD
IRDIAIENASMVVLNFTLQFLEPSERQALLDKIYQGLNPGGALVLSEKFS
FEDAKVGELLFNMHHDFKRANGYSELEISQKRSMLENVMLTDSVETHKAR
LHKAGFEHSELWFQCFNFGSLVALKAEDAA
Ligand information
Ligand IDGEK
InChIInChI=1S/C16H22N6O7S/c17-7(16(27)28)1-2-30(4-9(23)24)3-8-11(25)12(26)15(29-8)22-6-21-10-13(18)19-5-20-14(10)22/h5-8,11-12,15,25-26H,1-4,17H2,(H3-,18,19,20,23,24,27,28)/t7-,8+,11+,12+,15+,30-/m0/s1
InChIKeyVFFTYSZNZJBRBG-HEOPWLPUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](C[S+](CC[CH]([NH3+])C([O-])=O)CC([O-])=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[S@+](CC[C@@H](C(=O)[O-])[NH3+])CC(=O)[O-])O)O)N
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)C[S+](CCC(C(=O)[O-])[NH3+])CC(=O)[O-])O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](C[S@+](CC[C@H]([NH3+])C([O-])=O)CC([O-])=O)[C@@H](O)[C@H]3O
ACDLabs 12.01[O-]C(=O)C[S+](CCC(C([O-])=O)[NH3+])CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC16 H22 N6 O7 S
Name(2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate;
CARBOXY-S-ADENOSYLMETHIONINE
ChEMBL
DrugBank
ZINC
PDB chain4gek Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4gek Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function
Resolution1.5 Å
Binding residue
(original residue number in PDB)
F20 F28 Y39 G64 S66 D89 N90 D117 I118 N132 F133 F137 R199
Binding residue
(residue number reindexed from 1)
F3 F11 Y22 G47 S49 D72 N73 D100 I101 N115 F116 F120 R182
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.3.-
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0016743 carboxyl- or carbamoyltransferase activity
GO:1904047 S-adenosyl-L-methionine binding
Biological Process
GO:0002098 tRNA wobble uridine modification
GO:0032259 methylation

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:4gek, PDBe:4gek, PDBj:4gek
PDBsum4gek
PubMed23676670
UniProtC3T5M2

[Back to BioLiP]