Structure of PDB 5oo6 Chain B Binding Site BS02

Receptor Information
>5oo6 Chain B (length=148) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTE
EQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYING
TRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAGRGGYGK
Ligand information
Ligand IDMGT
InChIInChI=1S/C11H20N5O14P3/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(28-10)2-27-32(23,24)30-33(25,26)29-31(20,21)22/h4,6-7,10,17-18H,2-3H2,1H3,(H,23,24)(H,25,26)(H2,20,21,22)(H3,12,13,14,19)/t4-,6-,7-,10-/m1/s1
InChIKeyBUJQMJUTTBGELS-KQYNXXCUSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(N1C=2N=C(N)NC(=O)C=2N(C1)C)C(O)C3O
OpenEye OEToolkits 1.5.0CN1CN(C2=C1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341CN1CN([C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)C3=C1C(=O)NC(=N3)N
CACTVS 3.341CN1CN([CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O)C3=C1C(=O)NC(=N3)N
OpenEye OEToolkits 1.5.0CN1CN(C2=C1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O
FormulaC11 H20 N5 O14 P3
Name7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1234306
DrugBankDB03358
ZINCZINC000036753028
PDB chain5oo6 Chain B Residue 201 [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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PDB5oo6 Structural basis for mutually exclusive co-transcriptional nuclear cap-binding complexes with either NELF-E or ARS2.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		Y20 Y43 F83 R112 D114 R123 R127 Q133 V134
Binding residue
(residue number reindexed from 1)		Y17 Y40 F80 R109 D111 R120 R124 Q130 V131
Annotation score1
Enzymatic activity
Enzyme Commision number ?
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5oo6, PDBe:5oo6, PDBj:5oo6
PDBsum5oo6
PubMed29101316
UniProtP52298|NCBP2_HUMAN Nuclear cap-binding protein subunit 2 (Gene Name=NCBP2)

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