Structure of PDB 1d2h Chain C Binding Site BS01

Receptor Information
>1d2h Chain C (length=252) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVTSVDASDKM
LKYALKERWNRRKEPAFDKWVIEEANWLTLDKDVPAGDGFDAVICLGNSF
AHLPDSKGDQSEHRLALKNIASMVRPGGLLVIDHKNYDYILSTGCAPPGK
NIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGAGRDGAPGFSKFRL
SYYPHCLASFTELVQEAFGGRCQHSVLGDFKPYRPGQAYVPCYFIHVLKK
TG
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain1d2h Chain C Residue 3301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1d2h Mechanisms for auto-inhibition and forced product release in glycine N-methyltransferase: crystal structures of wild-type, mutant R175K and S-adenosylhomocysteine-bound R175K enzymes.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		D85 A86 S87 M90 N116 W117 S139 Y194
Binding residue
(residue number reindexed from 1)		D45 A46 S47 M50 N76 W77 S99 Y154
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) G137 H142 K175 Y194
Catalytic site (residue number reindexed from 1) G97 H102 K135 Y154
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:1d2h, PDBe:1d2h, PDBj:1d2h
PDBsum1d2h
PubMed10756111
UniProtP13255|GNMT_RAT Glycine N-methyltransferase (Gene Name=Gnmt)

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