Structure of PDB 7wub Chain A Binding Site BS03

Receptor Information
>7wub Chain A (length=576) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGT
GKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPA
IIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNR
PNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQV
ANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTM
DDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEH
PDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLT
MWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADR
VINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPD
EKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAI
RESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSD
NDIRKYEMFAQTLQQSRGFGSFRFPS
Ligand information
Ligand IDY6Y
InChIInChI=1S/C27H28N4O3S2/c1-19-16-22(11-14-25(19)20-9-12-24(13-10-20)36(2,32)33)34-18-26-29-30-27(35-23-7-3-4-8-23)31(26)21-6-5-15-28-17-21/h5-6,9-17,23H,3-4,7-8,18H2,1-2H3
InChIKeyUJGTUKMAJVCBIS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc(OCc2nnc(SC3CCCC3)n2c4cccnc4)ccc1c5ccc(cc5)[S](C)(=O)=O
OpenEye OEToolkits 2.0.7Cc1cc(ccc1c2ccc(cc2)S(=O)(=O)C)OCc3nnc(n3c4cccnc4)SC5CCCC5
FormulaC27 H28 N4 O3 S2
Name3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine
ChEMBLCHEMBL2311578
DrugBank
ZINCZINC000095598073
PDB chain7wub Chain F Residue 802 [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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PDB7wub Cryo-EM structure of dodecamer P97 at 2.99 Angstroms resolution
Resolution3.0 Å
Binding residue
(original residue number in PDB)		Q398 R453
Binding residue
(residue number reindexed from 1)		Q199 R254
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.4.6: vesicle-fusing ATPase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008289 lipid binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0019903 protein phosphatase binding
GO:0019904 protein domain specific binding
GO:0031593 polyubiquitin modification-dependent protein binding
GO:0031625 ubiquitin protein ligase binding
GO:0035800 deubiquitinase activator activity
GO:0036435 K48-linked polyubiquitin modification-dependent protein binding
GO:0042288 MHC class I protein binding
GO:0042802 identical protein binding
GO:0043531 ADP binding
GO:0044389 ubiquitin-like protein ligase binding
GO:0044877 protein-containing complex binding
GO:0140036 ubiquitin-modified protein reader activity
GO:1904288 BAT3 complex binding
GO:1990381 ubiquitin-specific protease binding
Biological Process
GO:0006281 DNA repair
GO:0006302 double-strand break repair
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006734 NADH metabolic process
GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport
GO:0006914 autophagy
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0006974 DNA damage response
GO:0010498 proteasomal protein catabolic process
GO:0010918 positive regulation of mitochondrial membrane potential
GO:0016236 macroautophagy
GO:0016567 protein ubiquitination
GO:0019079 viral genome replication
GO:0019985 translesion synthesis
GO:0030968 endoplasmic reticulum unfolded protein response
GO:0030970 retrograde protein transport, ER to cytosol
GO:0031334 positive regulation of protein-containing complex assembly
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0032510 endosome to lysosome transport via multivesicular body sorting pathway
GO:0033554 cellular response to stress
GO:0034605 cellular response to heat
GO:0035331 negative regulation of hippo signaling
GO:0035617 stress granule disassembly
GO:0036297 interstrand cross-link repair
GO:0036503 ERAD pathway
GO:0042981 regulation of apoptotic process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0045184 establishment of protein localization
GO:0045732 positive regulation of protein catabolic process
GO:0045879 negative regulation of smoothened signaling pathway
GO:0046034 ATP metabolic process
GO:0050807 regulation of synapse organization
GO:0051228 mitotic spindle disassembly
GO:0061857 endoplasmic reticulum stress-induced pre-emptive quality control
GO:0070842 aggresome assembly
GO:0071218 cellular response to misfolded protein
GO:0072389 flavin adenine dinucleotide catabolic process
GO:0090263 positive regulation of canonical Wnt signaling pathway
GO:0097352 autophagosome maturation
GO:0106300 protein-DNA covalent cross-linking repair
GO:0120186 negative regulation of protein localization to chromatin
GO:0140455 cytoplasm protein quality control
GO:1901224 positive regulation of non-canonical NF-kappaB signal transduction
GO:1903006 positive regulation of protein K63-linked deubiquitination
GO:1903007 positive regulation of Lys63-specific deubiquitinase activity
GO:1903715 regulation of aerobic respiration
GO:1903843 cellular response to arsenite ion
GO:1903862 positive regulation of oxidative phosphorylation
GO:1905634 regulation of protein localization to chromatin
GO:2000060 positive regulation of ubiquitin-dependent protein catabolic process
GO:2001171 positive regulation of ATP biosynthetic process
Cellular Component
GO:0000502 proteasome complex
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005811 lipid droplet
GO:0005829 cytosol
GO:0010494 cytoplasmic stress granule
GO:0032991 protein-containing complex
GO:0034098 VCP-NPL4-UFD1 AAA ATPase complex
GO:0034774 secretory granule lumen
GO:0035578 azurophil granule lumen
GO:0035861 site of double-strand break
GO:0036513 Derlin-1 retrotranslocation complex
GO:0043231 intracellular membrane-bounded organelle
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome
GO:0098978 glutamatergic synapse
GO:1904813 ficolin-1-rich granule lumen
GO:1904949 ATPase complex
GO:1990730 VCP-NSFL1C complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7wub, PDBe:7wub, PDBj:7wub
PDBsum7wub
PubMed
UniProtP55072|TERA_HUMAN Transitional endoplasmic reticulum ATPase (Gene Name=VCP)

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