Structure of PDB 8by6 Chain B Binding Site BS01

Receptor Information

>8by6 Chain B (length=152) Species: 9606 (Homo sapiens)

GLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTE
EQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYING
TRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLA
QN

Ligand information

• Ligand ID: GTG
• InChI: InChI=1S/C21H29N10O18P3/c1-29-5-31(15-9(29)17(37)28-21(23)26-15)19-13(35)11(33)7(47-19)3-45-51(40,41)49-52(42,43)48-50(38,39)44-2-6-10(32)12(34)18(46-6)30-4-24-8-14(30)25-20(22)27-16(8)36/h4-7,10-13,18-19,32-35H,2-3H2,1H3,(H8-,22,23,25,26,27,28,36,37,38,39,40,41,42,43)/p+1/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1
• InChIKey: FHHZHGZBHYYWTG-INFSMZHSSA-O
• SMILES:
  CACTVS 3.385: C[n+]1cn([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5C(=O)NC(=Nc45)N)[C@@H](O)[C@H]2O)c6N=C(N)NC(=O)c16
  CACTVS 3.385: C[n+]1cn([CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5C(=O)NC(=Nc45)N)[CH](O)[CH]2O)c6N=C(N)NC(=O)c16
  OpenEye OEToolkits 1.7.5: C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OP(=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O
  ACDLabs 10.04: O=C1NC(=Nc2c1[n+](cn2C3OC(C(O)C3O)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c5N=C(N)NC4=O)C(O)C6O)C)N
  OpenEye OEToolkits 1.7.5: C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O
• Formula: C21 H30 N10 O18 P3
• Name: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE;
  MRNA CAP ANALOG N7-METHYL GPPPG
• DrugBank: DB03958
• ZINC: ZINC000085547903
• PDB chain: 8by6 Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8by6 Structural basis for competitive binding of co-transcriptional classifier factors to the nuclear cap-binding complex
• Resolution: 3.19 Å
• Binding residue (original residue number in PDB): Y20 Y43 D114 W115 D116 R123 G126 R127 Q133 V134 Y138
• Binding residue (residue number reindexed from 1): Y17 Y40 D111 W112 D113 R120 G123 R124 Q130 V131 Y135
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0000339 RNA cap binding
• GO:0000340 RNA 7-methylguanosine cap binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0005515 protein binding
• GO:0017069 snRNA binding

Biological Process

• GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
• GO:0000380 alternative mRNA splicing, via spliceosome
• GO:0000398 mRNA splicing, via spliceosome
• GO:0002191 cap-dependent translational initiation
• GO:0006397 mRNA processing
• GO:0006406 mRNA export from nucleus
• GO:0006408 snRNA export from nucleus
• GO:0006417 regulation of translation
• GO:0006446 regulation of translational initiation
• GO:0008334 histone mRNA metabolic process
• GO:0008380 RNA splicing
• GO:0016071 mRNA metabolic process
• GO:0031047 regulatory ncRNA-mediated gene silencing
• GO:0031053 primary miRNA processing
• GO:0031124 mRNA 3'-end processing
• GO:0031442 positive regulation of mRNA 3'-end processing
• GO:0032968 positive regulation of transcription elongation by RNA polymerase II
• GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing
• GO:0035195 miRNA-mediated post-transcriptional gene silencing
• GO:0042789 mRNA transcription by RNA polymerase II
• GO:0045292 mRNA cis splicing, via spliceosome
• GO:0046833 positive regulation of RNA export from nucleus
• GO:0051028 mRNA transport

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005846 nuclear cap binding complex
• GO:0034518 RNA cap binding complex

External links

• PDB: RCSB:8by6, PDBe:8by6, PDBj:8by6
• PDBsum: 8by6
• PubMed: 38175753
• UniProt: P52298|NCBP2_HUMAN Nuclear cap-binding protein subunit 2 (Gene Name=NCBP2)