Structure of PDB 7vdq Chain B

Receptor sequence
>7vdqB (length=277) Species: 9606 (Homo sapiens) [Search protein sequence]
KYEKLEVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKELKHK
NIVRLHDVLHSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLL
KGLGFCHSRNVLHRDLKPQNLLINRNGELKLADFGLARAFGIPVRCYSAE
VVTLWYRPPDVLFGAKLYSTSIDMWSAGCIFAELANAGRPLFPGNDVDDQ
LKRIFRLLGTPTEEQWPSMTKLPDYKPYPMYPATTSLVNVVPKLNATGRD
LLQNLLKCNPVQRISAEEALQHPYFSD
3D structure
PDB7vdq Discovery and Optimization of Highly Selective Inhibitors of CDK5.
ChainB
Resolution2.91 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 64V B A31 E51 F80 C83 Q85 D86 K89 N131 D144 A20 E40 F69 C72 Q74 D75 K78 N120 D133
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:7vdq, PDBe:7vdq, PDBj:7vdq
PDBsum7vdq
PubMed35143203
UniProtQ00535|CDK5_HUMAN Cyclin-dependent kinase 5 (Gene Name=CDK5)

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