Structure of PDB 1unh Chain B Binding Site BS01

Receptor Information

>1unh Chain B (length=276) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

QKYEKLEKIYGTVFKAKNRHEIVALKRVRLDGVPSSALREICLLKELKHK
NIVRLHDVLHSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLL
KGLGFCHSRNVLHRDLKPQNLLINRNGELKLANFGLARAFGIPVRCYSAE
VVTLWYRPPDVLFGAKLYSTSIDMWSAGCIFAELANAGRPLFPGNDVDDQ
LKRIFRLLGTPTEEQWPSMTKLPDYKPYPMYPATTSLVNVVPKLNATGRD
LLQNLLKCNPVQRISAEEALQHPYFS

Ligand information

Ligand ID

IXM

InChI

InChI=1S/C16H11N3O2/c20-16-13(9-5-1-3-7-11(9)18-16)15-14(19-21)10-6-2-4-8-12(10)17-15/h1-8,17,21H,(H,18,20)/b15-13-,19-14+

InChIKey

HBDSHCUSXQATPO-BGBJRWHRSA-N

SMILES

Software	SMILES
ACDLabs 10.04	O=C2C(\c1ccccc1N2)=C4\C(=N\O)\c3ccccc3N4
OpenEye OEToolkits 1.5.0	c1ccc2c(c1)/C(=C/3\C(=N\O)\c4ccccc4N3)/C(=O)N2
CACTVS 3.341	ON=C1C(Nc2ccccc12)=C3C(=O)Nc4ccccc34
CACTVS 3.341	O/N=C1/C(Nc2ccccc12)=C3/C(=O)Nc4ccccc34
OpenEye OEToolkits 1.5.0	c1ccc2c(c1)C(=C3C(=NO)c4ccccc4N3)C(=O)N2

Formula

C16 H11 N3 O2

Name

(Z)-1H,1'H-[2,3']BIINDOLYLIDENE-3,2'-DIONE-3-OXIME;
INDIRUBIN-3'-MONOXIME

PDB chain

1unh Chain B Residue 1288 [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	1unh Mechanism of Cdk5/P25 Binding by Cdk Inhibitors
Resolution	2.35 Å
Binding residue (original residue number in PDB)	I10 A31 F80 F82 C83 D84 Q85 L133
Binding residue (residue number reindexed from 1)	I9 A24 F69 F71 C72 D73 Q74 L122
Annotation score	1
Binding affinity	MOAD: ic50=0.1uM

Enzymatic activity

Catalytic site (original residue number in PDB)	D126 K128 Q130 N131 N144 C157 T164
Catalytic site (residue number reindexed from 1)	D115 K117 Q119 N120 N133 C146 T153
Enzyme Commision number	2.7.11.1: non-specific serine/threonine protein kinase.

Gene Ontology

	Molecular Function
GO:0002039	p53 binding
GO:0004672	protein kinase activity
GO:0004674	protein serine/threonine kinase activity
GO:0004693	cyclin-dependent protein serine/threonine kinase activity
GO:0005176	ErbB-2 class receptor binding
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0008017	microtubule binding
GO:0016301	kinase activity
GO:0030549	acetylcholine receptor activator activity
GO:0043125	ErbB-3 class receptor binding
GO:0044024	histone H2AS1 kinase activity
GO:0048156	tau protein binding
GO:0050321	tau-protein kinase activity
GO:0051879	Hsp90 protein binding
GO:0106310	protein serine kinase activity

	Biological Process
GO:0000226	microtubule cytoskeleton organization
GO:0001764	neuron migration
GO:0001963	synaptic transmission, dopaminergic
GO:0006338	chromatin remodeling
GO:0006468	protein phosphorylation
GO:0006886	intracellular protein transport
GO:0006915	apoptotic process
GO:0007160	cell-matrix adhesion
GO:0007268	chemical synaptic transmission
GO:0007399	nervous system development
GO:0007409	axonogenesis
GO:0007416	synapse assembly
GO:0007519	skeletal muscle tissue development
GO:0008045	motor neuron axon guidance
GO:0008306	associative learning
GO:0008542	visual learning
GO:0014044	Schwann cell development
GO:0016079	synaptic vesicle exocytosis
GO:0016241	regulation of macroautophagy
GO:0016310	phosphorylation
GO:0016477	cell migration
GO:0018105	peptidyl-serine phosphorylation
GO:0018107	peptidyl-threonine phosphorylation
GO:0019233	sensory perception of pain
GO:0021537	telencephalon development
GO:0021549	cerebellum development
GO:0021695	cerebellar cortex development
GO:0021697	cerebellar cortex formation
GO:0021766	hippocampus development
GO:0021819	layer formation in cerebral cortex
GO:0021954	central nervous system neuron development
GO:0021987	cerebral cortex development
GO:0022038	corpus callosum development
GO:0030036	actin cytoskeleton organization
GO:0030182	neuron differentiation
GO:0030334	regulation of cell migration
GO:0030517	negative regulation of axon extension
GO:0030900	forebrain development
GO:0031175	neuron projection development
GO:0031397	negative regulation of protein ubiquitination
GO:0031914	negative regulation of synaptic plasticity
GO:0032801	receptor catabolic process
GO:0035249	synaptic transmission, glutamatergic
GO:0035418	protein localization to synapse
GO:0042220	response to cocaine
GO:0042981	regulation of apoptotic process
GO:0043113	receptor clustering
GO:0043525	positive regulation of neuron apoptotic process
GO:0045786	negative regulation of cell cycle
GO:0045861	negative regulation of proteolysis
GO:0045892	negative regulation of DNA-templated transcription
GO:0045956	positive regulation of calcium ion-dependent exocytosis
GO:0046826	negative regulation of protein export from nucleus
GO:0048148	behavioral response to cocaine
GO:0048167	regulation of synaptic plasticity
GO:0048488	synaptic vesicle endocytosis
GO:0048489	synaptic vesicle transport
GO:0048511	rhythmic process
GO:0048675	axon extension
GO:0048709	oligodendrocyte differentiation
GO:0048813	dendrite morphogenesis
GO:0051301	cell division
GO:0051402	neuron apoptotic process
GO:0051649	establishment of localization in cell
GO:0051726	regulation of cell cycle
GO:0051966	regulation of synaptic transmission, glutamatergic
GO:0060078	regulation of postsynaptic membrane potential
GO:0060079	excitatory postsynaptic potential
GO:0061001	regulation of dendritic spine morphogenesis
GO:0070509	calcium ion import
GO:0090314	positive regulation of protein targeting to membrane
GO:1903076	regulation of protein localization to plasma membrane
GO:1903421	regulation of synaptic vesicle recycling
GO:1904646	cellular response to amyloid-beta

	Cellular Component
GO:0000307	cyclin-dependent protein kinase holoenzyme complex
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0005874	microtubule
GO:0005886	plasma membrane
GO:0014069	postsynaptic density
GO:0016020	membrane
GO:0016533	protein kinase 5 complex
GO:0030027	lamellipodium
GO:0030054	cell junction
GO:0030175	filopodium
GO:0030424	axon
GO:0030425	dendrite
GO:0030426	growth cone
GO:0031594	neuromuscular junction
GO:0042995	cell projection
GO:0043005	neuron projection
GO:0043025	neuronal cell body
GO:0043204	perikaryon
GO:0045202	synapse
GO:0098793	presynapse

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:1unh, PDBe:1unh, PDBj:1unh
PDBsum	1unh
PubMed	15689152
UniProt	Q00535\|CDK5_HUMAN Cyclin-dependent kinase 5 (Gene Name=CDK5)

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