Structure of PDB 8dnf Chain D Binding Site BS01

Receptor Information
>8dnf Chain D (length=374) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKD
SYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEH
PVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGI
VMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFT
TTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIG
NERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSG
GTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLST
FQQMWISKQEYDESGPSIVHRKCF
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain8dnf Chain D Residue 401 [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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PDB8dnf Structural insights into actin isoforms.
Resolution3.38 Å
Binding residue
(original residue number in PDB)		S13 K17 K212 E213 G301 Y305 K335
Binding residue
(residue number reindexed from 1)		S13 K17 K212 E213 G301 Y305 K335
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.-
Gene Ontology
Molecular Function
GO:0005200 structural constituent of cytoskeleton
GO:0005515 protein binding
GO:0005522 profilin binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0019901 protein kinase binding
GO:0031625 ubiquitin protein ligase binding
GO:0042802 identical protein binding
GO:0098973 structural constituent of postsynaptic actin cytoskeleton
Biological Process
GO:0001525 angiogenesis
GO:0001738 morphogenesis of a polarized epithelium
GO:0007409 axonogenesis
GO:0010628 positive regulation of gene expression
GO:0030335 positive regulation of cell migration
GO:0035633 maintenance of blood-brain barrier
GO:0045214 sarcomere organization
GO:0048870 cell motility
GO:0051492 regulation of stress fiber assembly
GO:0051893 regulation of focal adhesion assembly
GO:0070527 platelet aggregation
GO:0071346 cellular response to type II interferon
GO:0090303 positive regulation of wound healing
GO:0098974 postsynaptic actin cytoskeleton organization
GO:0120192 tight junction assembly
GO:0150111 regulation of transepithelial transport
GO:1900242 regulation of synaptic vesicle endocytosis
GO:1902396 protein localization to bicellular tight junction
Cellular Component
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005884 actin filament
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0005925 focal adhesion
GO:0015629 actin cytoskeleton
GO:0016020 membrane
GO:0030016 myofibril
GO:0030424 axon
GO:0031941 filamentous actin
GO:0035267 NuA4 histone acetyltransferase complex
GO:0043296 apical junction complex
GO:0044305 calyx of Held
GO:0045177 apical part of cell
GO:0045202 synapse
GO:0045335 phagocytic vesicle
GO:0070062 extracellular exosome
GO:0072562 blood microparticle
GO:0097433 dense body
GO:0098685 Schaffer collateral - CA1 synapse
GO:0120220 basal body patch

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8dnf, PDBe:8dnf, PDBj:8dnf
PDBsum8dnf
PubMed36790143
UniProtP63261|ACTG_HUMAN Actin, cytoplasmic 2 (Gene Name=ACTG1)

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