Structure of PDB 1unh Chain A Binding Site BS01

Receptor Information
>1unh Chain A (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 IDIXM
InChIInChI=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+
InChIKeyHBDSHCUSXQATPO-BGBJRWHRSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C2C(\c1ccccc1N2)=C4\C(=N\O)\c3ccccc3N4
OpenEye OEToolkits 1.5.0c1ccc2c(c1)/C(=C/3\C(=N\O)\c4ccccc4N3)/C(=O)N2
CACTVS 3.341ON=C1C(Nc2ccccc12)=C3C(=O)Nc4ccccc34
CACTVS 3.341O/N=C1/C(Nc2ccccc12)=C3/C(=O)Nc4ccccc34
OpenEye OEToolkits 1.5.0c1ccc2c(c1)C(=C3C(=NO)c4ccccc4N3)C(=O)N2
FormulaC16 H11 N3 O2
Name(Z)-1H,1'H-[2,3']BIINDOLYLIDENE-3,2'-DIONE-3-OXIME;
INDIRUBIN-3'-MONOXIME
ChEMBLCHEMBL216543
DrugBankDB02052
ZINCZINC000100001998
PDB chain1unh Chain A Residue 1288 [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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PDB1unh Mechanism of Cdk5/P25 Binding by Cdk Inhibitors
Resolution2.35 Å
Binding residue
(original residue number in PDB)		I10 A31 F80 F82 C83 D84 Q85 D86 L133
Binding residue
(residue number reindexed from 1)		I9 A24 F69 F71 C72 D73 Q74 D75 L122
Annotation score1
Binding affinityMOAD: ic50=0.1uM
PDBbind-CN: -logKd/Ki=7.00,IC50=0.10uM
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
PDBsum1unh
PubMed15689152
UniProtQ00535|CDK5_HUMAN Cyclin-dependent kinase 5 (Gene Name=CDK5)

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