Structure of PDB 4gom Chain E Binding Site BS01

Receptor Information
>4gom Chain E (length=244) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYIL
ADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQ
DPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFA
EKAQNAFFYCESYADSMARADDASVVYCDPPYAPLSFTLEQQAHLAEIAE
GLVERHIPVLISNHDTMLTREWYQRAKLHVVKVKVDELLALYKP
Ligand information
Ligand ID0Y0
InChIInChI=1S/C14H21N7O5/c15-6(14(24)25)1-2-17-3-7-9(22)10(23)13(26-7)21-5-20-8-11(16)18-4-19-12(8)21/h4-7,9-10,13,17,22-23H,1-3,15H2,(H,24,25)(H2,16,18,19)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyWSOGVCAFRBSBRE-WFMPWKQPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CNCC[C@@H](C(=O)O)N)O)O)N
CACTVS 3.370N[CH](CCNC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 12.01O=C(O)C(N)CCNCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CNCCC(C(=O)O)N)O)O)N
CACTVS 3.370N[C@@H](CCNC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
FormulaC14 H21 N7 O5
Name5'-{[(3S)-3-amino-3-carboxypropyl]amino}-5'-deoxyadenosine
ChEMBLCHEMBL2018849
DrugBank
ZINCZINC000039470870
PDB chain4gom Chain E Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4gom Structural Basis of Selective N-6 adenine methyltransferase Inhibition by Transition State Mimic
Resolution2.45 Å
Binding residue
(original residue number in PDB)		A11 F35 D54 I55 Y165 D181 P183 Y184
Binding residue
(residue number reindexed from 1)		A9 F33 D52 I53 Y163 D179 P181 Y182
Annotation score3
Enzymatic activity
Enzyme Commision number 2.1.1.72: site-specific DNA-methyltransferase (adenine-specific).
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity
GO:0043565 sequence-specific DNA binding
GO:1904047 S-adenosyl-L-methionine binding
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006298 mismatch repair
GO:0009307 DNA restriction-modification system
GO:0009411 response to UV
GO:0032259 methylation
GO:1902328 bacterial-type DNA replication initiation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4gom, PDBe:4gom, PDBj:4gom
PDBsum4gom
PubMed
UniProtP0AEE8|DMA_ECOLI DNA adenine methylase (Gene Name=dam)

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