Structure of PDB 4m9s Chain D Binding Site BS03

Receptor Information
>4m9s Chain D (length=511) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLCEIECRALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTR
LERIANFLRIYRRQASELGPLIDFFNYNNQSHLADFLEDYIDFAINEPDL
LRPVVIAPQFSRQMLDRKLLLGNVPKQMTCYIREYHVDRVIKKLDEMCDL
DSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKST
FDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFD
DVVQEETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYD
FLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQ
LNNKLESRGLVGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMP
PGVDIPVKLWSCVIPVLDDEVADRLKRLSKRGALLSGKRMPVLTFKIDHI
IHMFLKHVVDAQTIANGISILEQRLLEIGNNNETVIRPEDFPKFMQLHQK
FYDSLKNFACC
Ligand information
Ligand IDATP
InChIInChI=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
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(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 3.341Nc1ncnc2n(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
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain4m9s Chain D Residue 602 [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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PDB4m9s Mechanistic insights into CED-4-mediated activation of CED-3.
Resolution3.207 Å
Binding residue
(original residue number in PDB)		M128 Y131 G164 K165 S166 V167 R273 F301 P330 A331 M334 P368 Y369
Binding residue
(residue number reindexed from 1)		M128 Y131 G164 K165 S166 V167 R273 F301 P330 A331 M334 P368 Y369
Annotation score4
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4m9s, PDBe:4m9s, PDBj:4m9s
PDBsum4m9s
PubMed24065769
UniProtP30429|CED4_CAEEL Cell death protein 4 (Gene Name=ced-4)

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