Structure of PDB 8jo0 Chain D Binding Site BS01
Receptor Information
>8jo0 Chain D (length=391) Species:
6239
(Caenorhabditis elegans) [
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RQMLDRKLLLGNVPKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRA
GSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLML
KSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWA
QELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPV
GEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRGLV
GVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIPVKLWS
CVIPVEQLDDEVADRLKRLSKRGALLSGKRMPVLTFKIDHIIHMFLKHVV
DAQTIANGISILEQRLLEITVIRPEDFPKFMQLHQKFYDSL
Ligand information
Ligand ID
ATP
InChI
InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKey
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341
Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04
O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341
Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
Formula
C10 H16 N5 O13 P3
Name
ADENOSINE-5'-TRIPHOSPHATE
ChEMBL
CHEMBL14249
DrugBank
DB00171
ZINC
ZINC000004261765
PDB chain
8jo0 Chain D Residue 602 [
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Receptor-Ligand Complex Structure
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PDB
8jo0
Structural insights into CED-3 activation.
Resolution
3.6 Å
Binding residue
(original residue number in PDB)
G162 G164 K165 S166 V167 R273 F301 Y305 P330 A331 M334 P368 Y369
Binding residue
(residue number reindexed from 1)
G51 G53 K54 S55 V56 R162 F190 Y194 P219 A220 M223 P257 Y258
Annotation score
4
Enzymatic activity
Enzyme Commision number
?
Gene Ontology
Molecular Function
GO:0000287
magnesium ion binding
GO:0005515
protein binding
GO:0005524
ATP binding
GO:0008656
cysteine-type endopeptidase activator activity involved in apoptotic process
GO:0016505
peptidase activator activity involved in apoptotic process
GO:0042802
identical protein binding
GO:0043531
ADP binding
GO:0046872
metal ion binding
GO:0051432
BH1 domain binding
GO:0051434
BH3 domain binding
GO:0061133
endopeptidase activator activity
GO:0089720
caspase binding
Biological Process
GO:0006915
apoptotic process
GO:0006919
activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0008361
regulation of cell size
GO:0009792
embryo development ending in birth or egg hatching
GO:0010954
positive regulation of protein processing
GO:0030042
actin filament depolymerization
GO:0030155
regulation of cell adhesion
GO:0031647
regulation of protein stability
GO:0040034
regulation of development, heterochronic
GO:0042981
regulation of apoptotic process
GO:0043065
positive regulation of apoptotic process
GO:0046716
muscle cell cellular homeostasis
GO:0048598
embryonic morphogenesis
GO:0050829
defense response to Gram-negative bacterium
GO:0097202
activation of cysteine-type endopeptidase activity
GO:1900118
negative regulation of execution phase of apoptosis
GO:1902742
apoptotic process involved in development
GO:1904747
positive regulation of apoptotic process involved in development
GO:1905808
positive regulation of synapse pruning
Cellular Component
GO:0005634
nucleus
GO:0005737
cytoplasm
GO:0005739
mitochondrion
GO:0005829
cytosol
GO:0008303
caspase complex
GO:0016020
membrane
GO:0032991
protein-containing complex
GO:0048471
perinuclear region of cytoplasm
View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:8jo0
,
PDBe:8jo0
,
PDBj:8jo0
PDBsum
8jo0
PubMed
37402593
UniProt
P30429
|CED4_CAEEL Cell death protein 4 (Gene Name=ced-4)
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