Structure of PDB 7rli Chain L Binding Site BS01

Receptor Information
>7rli Chain L (length=735) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCI
VLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPID
DTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDP
SPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMV
ELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLIN
GPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEV
ERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIG
IPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAAL
QAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVE
VPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPP
GCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAA
PCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFII
GATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDV
DLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIVPEIRRDHFEEAM
RFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPS
Ligand information
Ligand IDJDP
InChIInChI=1S/C24H23N5O2/c1-15-12-18-17(22(25)30)8-5-9-21(18)29(15)24-27-20-10-11-31-14-19(20)23(28-24)26-13-16-6-3-2-4-7-16/h2-9,12H,10-11,13-14H2,1H3,(H2,25,30)(H,26,27,28)
InChIKeyRDALZZCKQFLGJP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c5cccc(CNc3nc(n2c1cccc(C(=O)N)c1cc2C)nc4c3COCC4)c5
CACTVS 3.385Cc1cc2c(cccc2C(N)=O)n1c3nc4CCOCc4c(NCc5ccccc5)n3
OpenEye OEToolkits 2.0.6Cc1cc2c(cccc2n1c3nc4c(c(n3)NCc5ccccc5)COCC4)C(=O)N
FormulaC24 H23 N5 O2
Name1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide
ChEMBLCHEMBL3747513
DrugBankDB16874
ZINCZINC000208076131
PDB chain7rli Chain L Residue 901 [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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PDB7rli AAA+ ATPase p97/VCP mutants and inhibitor binding disrupt inter-domain coupling and subsequent allosteric activation.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		D478 I479 G521 C522 G523 L526 A655 I656 A659 N660 G684 A685 T688
Binding residue
(residue number reindexed from 1)		D458 I459 G501 C502 G503 L506 A635 I636 A639 N640 G664 A665 T668
Annotation score1
Binding affinityBindingDB: IC50=1030nM,Ki=26nM
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:7rli, PDBe:7rli, PDBj:7rli
PDBsum7rli
PubMed34520757
UniProtP55072|TERA_HUMAN Transitional endoplasmic reticulum ATPase (Gene Name=VCP)

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