Structure of PDB 6nt2 Chain B Binding Site BS01

Receptor Information
>6nt2 Chain B (length=330) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PNAEDMTSKDYYFDSYAHFGIHEEMLKDEVRTLTYRNSMFHNRHLFKDKV
VLDVGSGTGILCMFAAKAGARKVIGIECSSISDYAVKIVKANKLDHVVTI
IKGKVEEVELPVEKVDIIISEWMGYCLFYESMLNTVLYARDKWLAPDGLI
FPDRATLYVTAIEDRQYKDYKIHWWENVYGFDMSCIKDVAIKEPLVDVVD
PKQLVTNACLIKEVDIYTVKVEDLTFTSPFCLQVKRNDYVHALVAYFNIE
FTRCHKRTGFSTSPESPYTHWKQTVFYMEDYLTVKTGEEIFGTIGMRPNA
KNNRDLDFTIDLDFKGQLCELSCSTDYRMR
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 chain6nt2 Chain B Residue 401 [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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PDB6nt2 Anti-tumor Activity of the Type I PRMT Inhibitor, GSK3368715, Synergizes with PRMT5 Inhibition through MTAP Loss.
Resolution2.48 Å
Binding residue
(original residue number in PDB)		Y57 M66 R72 G96 I101 L102 E118 C119 K145 V146 E147 M173 T176
Binding residue
(residue number reindexed from 1)		Y16 M25 R31 G55 I60 L61 E77 C78 K104 V105 E106 M132 T135
Annotation score5
Binding affinityBindingDB: IC50=550nM
Enzymatic activity
Enzyme Commision number 2.1.1.319: type I protein arginine methyltransferase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008170 N-methyltransferase activity
GO:0008276 protein methyltransferase activity
GO:0008327 methyl-CpG binding
GO:0016274 protein-arginine N-methyltransferase activity
GO:0019899 enzyme binding
GO:0035241 protein-arginine omega-N monomethyltransferase activity
GO:0035242 protein-arginine omega-N asymmetric methyltransferase activity
GO:0042054 histone methyltransferase activity
GO:0042802 identical protein binding
GO:0044020 histone H4R3 methyltransferase activity
GO:0048273 mitogen-activated protein kinase p38 binding
GO:0106080 GATOR1 complex binding
GO:1904047 S-adenosyl-L-methionine binding
Biological Process
GO:0001701 in utero embryonic development
GO:0006338 chromatin remodeling
GO:0006479 protein methylation
GO:0006974 DNA damage response
GO:0007166 cell surface receptor signaling pathway
GO:0008284 positive regulation of cell population proliferation
GO:0008380 RNA splicing
GO:0018216 peptidyl-arginine methylation
GO:0019082 viral protein processing
GO:0030510 regulation of BMP signaling pathway
GO:0031175 neuron projection development
GO:0032259 methylation
GO:0045648 positive regulation of erythrocyte differentiation
GO:0045652 regulation of megakaryocyte differentiation
GO:0045653 negative regulation of megakaryocyte differentiation
GO:0045727 positive regulation of translation
GO:0046329 negative regulation of JNK cascade
GO:0046985 positive regulation of hemoglobin biosynthetic process
GO:0048738 cardiac muscle tissue development
GO:0051260 protein homooligomerization
GO:0061431 cellular response to methionine
GO:1900745 positive regulation of p38MAPK cascade
GO:1904263 positive regulation of TORC1 signaling
GO:1905168 positive regulation of double-strand break repair via homologous recombination
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005829 cytosol
GO:0016020 membrane
GO:0034709 methylosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6nt2, PDBe:6nt2, PDBj:6nt2
PDBsum6nt2
PubMed31257072
UniProtQ99873|ANM1_HUMAN Protein arginine N-methyltransferase 1 (Gene Name=PRMT1)

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