Structure of PDB 3vc2 Chain K Binding Site BS01

Receptor Information
>3vc2 Chain K (length=263) Species: 100226 (Streptomyces coelicolor A3(2)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PATPYQEDIARYWNNELYHHHYGIGPVDRAALGDPEHSEYEKKVIAELHR
LESAQAEFLMDHLGQAGPDDTLVDAGCGRGGSMVMAHRRFGSRVEGVTLS
AAQADFGNRRARELRIDDHVRSRVCNMLDTPFDKGAVTASWNNESTMYVD
LHDLFSEHSRFLKVGGRYVTITGCWNPRYGQPSKWVSQINAHFECNIHSR
REYLRAMADNRLVPHTIVDLTPDTLPYWELRATSSLVTGIEKAFIESYRD
GSFQYVLIAADRV
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 chain3vc2 Chain K Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vc2 Structure of Geranyl Diphosphate C-Methyltransferase from Streptomyces coelicolor and Implications for the Mechanism of Isoprenoid Modification.
Resolution2.046 Å
Binding residue
(original residue number in PDB)		Q22 W29 H48 H49 H50 G105 G107 T127 L128 Q132 C154 N155 M156 N172 Y177
Binding residue
(residue number reindexed from 1)		Q6 W13 H19 H20 H21 G76 G78 T98 L99 Q103 C125 N126 M127 N143 Y148
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.255: geranyl diphosphate 2-C-methyltransferase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0008168 methyltransferase activity
GO:0008169 C-methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:1904047 S-adenosyl-L-methionine binding
Biological Process
GO:0032259 methylation
GO:0042214 terpene metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3vc2, PDBe:3vc2, PDBj:3vc2
PDBsum3vc2
PubMed22455498
UniProtQ9F1Y5|GPPMT_STRCO Geranyl diphosphate 2-C-methyltransferase (Gene Name=SCO7701)

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