Structure of PDB 7rlj Chain B Binding Site BS02

Receptor Information
>7rlj Chain B (length=728) 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
RFARRSVSDNDIRKYEMFAQTLQQSRGF
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 chain7rlj Chain B Residue 803 [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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PDB7rlj AAA+ ATPase p97/VCP mutants and inhibitor binding disrupt inter-domain coupling and subsequent allosteric activation.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		V474 D478 I479 G523 L526 A685
Binding residue
(residue number reindexed from 1)		V454 D458 I459 G503 L506 A665
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:7rlj, PDBe:7rlj, PDBj:7rlj
PDBsum7rlj
PubMed34520757
UniProtP55072|TERA_HUMAN Transitional endoplasmic reticulum ATPase (Gene Name=VCP)

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