Structure of PDB 5cd1 Chain D Binding Site BS02

Receptor Information
>5cd1 Chain D (length=281) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVAYEELIKEGDTAILSLGHGAMVAVRVQRGAQTQTRHGVLRHSVDLIG
RPFGSKVTCGRGGWVYVLHPTPELWTLNLPHRTQILYSTDIALITMMLEL
RPGSVVCESGTGSGSVSHAIIRTIAPTGHLHTVEFHQQRAEKAREEFQEH
RVGRWVTVRTQDVCRSGFGVSHVADAVFLDIPSPWEAVGHAWDALKVEGG
RFCSFSPCIEQVQRTCQALAARGFSELSTLEVLPQVYNVRTVSLPPPDLG
TGDTSPFRSGTPMKEAVGHTGYLTFATKTPG
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 chain5cd1 Chain D Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5cd1 Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA3(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		T84 G111 S116 V117 E135 F136 R140 D163 D181 I182
Binding residue
(residue number reindexed from 1)		T83 G110 S115 V116 E134 F135 R139 D162 D180 I181
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.-
2.1.1.220: tRNA (adenine(58)-N(1))-methyltransferase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0061953 mRNA (adenine-N1-)-methyltransferase activity
GO:0160107 tRNA (adenine(58)-N1)-methyltransferase activity
Biological Process
GO:0006397 mRNA processing
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0031515 tRNA (m1A) methyltransferase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5cd1, PDBe:5cd1, PDBj:5cd1
PDBsum5cd1
PubMed26470919
UniProtQ96FX7|TRM61_HUMAN tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A (Gene Name=TRMT61A)

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