Structure of PDB 5xf4 Chain H Binding Site BS03

Receptor Information
>5xf4 Chain H (length=95) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRL
AHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
Ligand information
Ligand IDRUD
InChIInChI=1S/C10H12O2.C6H12N3P.2ClH.Ru/c1-8-2-4-9(5-3-8)6-7-10(11)12;1-7-2-9-3-8(1)5-10(4-7)6-9;;;/h2-5H,6-7H2,1H3,(H,11,12);1-6H2;2*1H;/q;;;;+1/p-1
InChIKeyUZIJOIXYBLAWLW-UHFFFAOYSA-M
SMILES
SoftwareSMILES
ACDLabs 12.01[Ru](P13CN2CN(C1)CN(C2)C3)(Cl)Cl.c1(C)ccc(cc1)CCC(=O)O
OpenEye OEToolkits 2.0.4Cc1ccc(cc1)CCC(=O)O.C1N2CN3CN1C[P](C2)(C3)[Ru](Cl)Cl
CACTVS 3.385Cc1ccc(CCC(O)=O)cc1.Cl[Ru]Cl.C2N3CN4CN2CP(C3)C4
FormulaC16 H24 Cl2 N3 O2 P Ru
Name[ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2
ChEMBL
DrugBank
ZINC
PDB chain5xf4 Chain H 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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PDB5xf4 Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation
Resolution2.87 Å
Binding residue
(original residue number in PDB)		E102 K105 H106
Binding residue
(residue number reindexed from 1)		E75 K78 H79
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001530 lipopolysaccharide binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0030527 structural constituent of chromatin
GO:0046982 protein heterodimerization activity
Biological Process
GO:0002227 innate immune response in mucosa
GO:0006325 chromatin organization
GO:0006334 nucleosome assembly
GO:0010804 negative regulation of tumor necrosis factor-mediated signaling pathway
GO:0019731 antibacterial humoral response
GO:0031640 killing of cells of another organism
GO:0042742 defense response to bacterium
GO:0050829 defense response to Gram-negative bacterium
GO:0050830 defense response to Gram-positive bacterium
GO:0061644 protein localization to CENP-A containing chromatin
GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide
Cellular Component
GO:0000786 nucleosome
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0043505 CENP-A containing nucleosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5xf4, PDBe:5xf4, PDBj:5xf4
PDBsum5xf4
PubMed29146919
UniProtP06899|H2B1J_HUMAN Histone H2B type 1-J (Gene Name=H2BC11)

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