Structure of PDB 8dnf Chain C Binding Site BS01

Receptor Information

>8dnf Chain C (length=374) Species: 9606 (Homo sapiens)

EEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKD
SYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEH
PVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGI
VMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFT
TTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIG
NERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSG
GTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLST
FQQMWISKQEYDESGPSIVHRKCF

Ligand information

• Ligand ID: ADP
• InChI: InChI=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
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(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 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 8dnf Chain C Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dnf Structural insights into actin isoforms.
• Resolution: 3.38 Å
• Binding residue (original residue number in PDB): G12 S13 K17 K212 E213 G301 K335
• Binding residue (residue number reindexed from 1): G12 S13 K17 K212 E213 G301 K335
• Annotation score: 5

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

External links

• PDB: RCSB:8dnf, PDBe:8dnf, PDBj:8dnf
• PDBsum: 8dnf
• PubMed: 36790143
• UniProt: P63261|ACTG_HUMAN Actin, cytoplasmic 2 (Gene Name=ACTG1)