Structure of PDB 8dnh Chain B Binding Site BS01

Receptor Information

>8dnh Chain B (length=374) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

DDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKD
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

Software	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

PDB chain

8dnh Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	8dnh Structural insights into actin isoforms.
Resolution	2.99 Å
Binding residue (original residue number in PDB)	G12 K17 G155 E213 G301 Y305
Binding residue (residue number reindexed from 1)	G12 K17 G155 E213 G301 Y305
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:0005524	ATP binding
GO:0016787	hydrolase activity
GO:0016887	ATP hydrolysis activity
GO:0019894	kinesin binding
GO:0019901	protein kinase binding
GO:0030957	Tat protein binding
GO:0031492	nucleosomal DNA binding
GO:0042802	identical protein binding
GO:0048156	tau protein binding
GO:0050998	nitric-oxide synthase binding
GO:0098973	structural constituent of postsynaptic actin cytoskeleton

	Biological Process
GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0001738	morphogenesis of a polarized epithelium
GO:0006338	chromatin remodeling
GO:0006357	regulation of transcription by RNA polymerase II
GO:0007010	cytoskeleton organization
GO:0007163	establishment or maintenance of cell polarity
GO:0007409	axonogenesis
GO:0008284	positive regulation of cell population proliferation
GO:0021762	substantia nigra development
GO:0022898	regulation of transmembrane transporter activity
GO:0030071	regulation of mitotic metaphase/anaphase transition
GO:0032091	negative regulation of protein binding
GO:0034333	adherens junction assembly
GO:0035633	maintenance of blood-brain barrier
GO:0042981	regulation of apoptotic process
GO:0045176	apical protein localization
GO:0045582	positive regulation of T cell differentiation
GO:0045596	negative regulation of cell differentiation
GO:0045597	positive regulation of cell differentiation
GO:0045663	positive regulation of myoblast differentiation
GO:0045893	positive regulation of DNA-templated transcription
GO:0048870	cell motility
GO:0051621	regulation of norepinephrine uptake
GO:0051623	positive regulation of norepinephrine uptake
GO:0051726	regulation of cell cycle
GO:0070316	regulation of G0 to G1 transition
GO:0070527	platelet aggregation
GO:0071896	protein localization to adherens junction
GO:0072749	cellular response to cytochalasin B
GO:0098974	postsynaptic actin cytoskeleton organization
GO:0150111	regulation of transepithelial transport
GO:1900242	regulation of synaptic vesicle endocytosis
GO:1902459	positive regulation of stem cell population maintenance
GO:1903076	regulation of protein localization to plasma membrane
GO:1905168	positive regulation of double-strand break repair via homologous recombination
GO:2000045	regulation of G1/S transition of mitotic cell cycle
GO:2000779	regulation of double-strand break repair
GO:2000781	positive regulation of double-strand break repair
GO:2000819	regulation of nucleotide-excision repair

	Cellular Component
GO:0000776	kinetochore
GO:0000785	chromatin
GO:0000786	nucleosome
GO:0005615	extracellular space
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0005856	cytoskeleton
GO:0005884	actin filament
GO:0005886	plasma membrane
GO:0005903	brush border
GO:0005911	cell-cell junction
GO:0005912	adherens junction
GO:0005925	focal adhesion
GO:0015629	actin cytoskeleton
GO:0016020	membrane
GO:0016363	nuclear matrix
GO:0016514	SWI/SNF complex
GO:0016586	RSC-type complex
GO:0030027	lamellipodium
GO:0030424	axon
GO:0030863	cortical cytoskeleton
GO:0031982	vesicle
GO:0032991	protein-containing complex
GO:0035060	brahma complex
GO:0035267	NuA4 histone acetyltransferase complex
GO:0036464	cytoplasmic ribonucleoprotein granule
GO:0043296	apical junction complex
GO:0044305	calyx of Held
GO:0045202	synapse
GO:0070062	extracellular exosome
GO:0070160	tight junction
GO:0071564	npBAF complex
GO:0071565	nBAF complex
GO:0072562	blood microparticle
GO:0097433	dense body
GO:0098685	Schaffer collateral - CA1 synapse
GO:0098793	presynapse
GO:0098871	postsynaptic actin cytoskeleton
GO:0098978	glutamatergic synapse
GO:0140092	bBAF complex
GO:0140288	GBAF complex
GO:1990904	ribonucleoprotein complex

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External links

PDB	RCSB:8dnh, PDBe:8dnh, PDBj:8dnh
PDBsum	8dnh
PubMed	36790143
UniProt	P60709\|ACTB_HUMAN Actin, cytoplasmic 1 (Gene Name=ACTB)

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