Structure of PDB 6l8u Chain D Binding Site BS01

Receptor Information
>6l8u Chain D (length=228) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PGAAPFGNFPHYSRFHPPEQRLRLLPPELLRQLFPESPENGPILGLDVGC
NSGDLSVALYKHFLSLASREFRLLCCDIDPVLVKRAEKECPFPDALTFIT
LDFMNQRTRKVLLSSFLSQFGRSVFDIGFCMSITMWIHLNHGDHGLWEFL
AHLSSLCHYLLVEPQPWKCYRAAARRLRKLGLHDFDHFHSLAIRGDMPNQ
IVQILTQDHGMELICCFGNDRSLLLFRA
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 chain6l8u Chain D Residue 1001 [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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PDB6l8u Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.
Resolution2.925 Å
Binding residue
(original residue number in PDB)		F31 G32 N33 R46 G74 N76 L80 D110 I111 D135 F136 S165 I166
Binding residue
(residue number reindexed from 1)		F6 G7 N8 R21 G49 N51 L55 D77 I78 D102 F103 S132 I133
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008171 O-methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0008175 tRNA methyltransferase activity
GO:0070883 pre-miRNA binding
GO:0090486 small RNA 2'-O-methyltransferase activity
Biological Process
GO:0001510 RNA methylation
GO:0010586 miRNA metabolic process
GO:0030488 tRNA methylation
GO:0031054 pre-miRNA processing
GO:0032259 methylation
GO:2000632 negative regulation of pre-miRNA processing
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:6l8u, PDBe:6l8u, PDBj:6l8u
PDBsum6l8u
PubMed31919512
UniProtQ7Z5W3|BN3D2_HUMAN RNA 5'-monophosphate methyltransferase (Gene Name=BCDIN3D)

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