Structure of PDB 1nbi Chain A Binding Site BS01

Receptor Information
>1nbi Chain A (length=275) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGT
GVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRKEPAFDKWVIEEANW
LTLDKDVPAGDGFDAVICLGNSFAHLPDSKGDQSEHRLALKNIASMVRPG
GLLVIDHKNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVT
LDYTVQVPGAGRDGAPGFSKFRLSYYPHCLASFTELVQEAFGGRCQHSVL
GDFKPYRPGQAYVPCYFIHVLKKTG
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain1nbi Chain A Residue 293 [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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PDB1nbi Catalytic mechanism of glycine N-methyltransferase
Resolution3.0 Å
Binding residue
(original residue number in PDB)		Y21 W30 R40 V69 D85 A86 S87 M90 N116 W117 S139 H142 Y194
Binding residue
(residue number reindexed from 1)		Y4 W13 R23 V52 D68 A69 S70 M73 N99 W100 S122 H125 Y177
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) Y21 G137 H142 K175 Y194
Catalytic site (residue number reindexed from 1) Y4 G120 H125 K158 Y177
Enzyme Commision number 2.1.1.20: glycine N-methyltransferase.
Gene Ontology
Molecular Function
GO:0005542 folic acid binding
GO:0008168 methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0016594 glycine binding
GO:0017174 glycine N-methyltransferase activity
GO:0042802 identical protein binding
GO:0098603 selenol Se-methyltransferase activity
GO:1904047 S-adenosyl-L-methionine binding
Biological Process
GO:0005977 glycogen metabolic process
GO:0006111 regulation of gluconeogenesis
GO:0006544 glycine metabolic process
GO:0006555 methionine metabolic process
GO:0006730 one-carbon metabolic process
GO:0032259 methylation
GO:0046498 S-adenosylhomocysteine metabolic process
GO:0046500 S-adenosylmethionine metabolic process
GO:0051289 protein homotetramerization
GO:1901052 sarcosine metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0034708 methyltransferase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1nbi, PDBe:1nbi, PDBj:1nbi
PDBsum1nbi
PubMed12859184
UniProtP13255|GNMT_RAT Glycine N-methyltransferase (Gene Name=Gnmt)

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