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- PDB-7vdp: The structure of cyclin-dependent kinase 5 (CDK5) in complex with... -

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Basic information

Entry
Database: PDB / ID: 7vdp
TitleThe structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1
Components
  • Cyclin-dependent kinase 5 activator 1, p25
  • Cyclin-dependent-like kinase 5
KeywordsTRANSFERASE / CDK5 / p25
Function / homology
Function and homology information


superior olivary nucleus maturation / acetylcholine receptor activator activity / protein kinase 5 complex / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / regulation of cell cycle phase transition / Activated NTRK2 signals through CDK5 / positive regulation of calcium ion-dependent exocytosis ...superior olivary nucleus maturation / acetylcholine receptor activator activity / protein kinase 5 complex / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / regulation of cell cycle phase transition / Activated NTRK2 signals through CDK5 / positive regulation of calcium ion-dependent exocytosis / layer formation in cerebral cortex / negative regulation of axon extension / neuron cell-cell adhesion / corpus callosum development / receptor catabolic process / cerebellar cortex formation / protein localization to synapse / regulation of dendritic spine morphogenesis / CRMPs in Sema3A signaling / NGF-stimulated transcription / ErbB-3 class receptor binding / synaptic transmission, dopaminergic / embryo development ending in birth or egg hatching / negative regulation of protein export from nucleus / motor neuron axon guidance / cyclin-dependent protein serine/threonine kinase activator activity / axon extension / axonal fasciculation / calcium ion import / regulation of synaptic vesicle cycle / regulation of synaptic vesicle recycling / phosphorylation / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of neuron differentiation / tau-protein kinase activity / synaptic vesicle transport / dendrite morphogenesis / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / receptor clustering / central nervous system neuron development / synaptic vesicle exocytosis / negative regulation of cell cycle / oligodendrocyte differentiation / synaptic vesicle endocytosis / protein kinase activator activity / positive regulation of protein targeting to membrane / DARPP-32 events / alpha-tubulin binding / regulation of macroautophagy / beta-tubulin binding / ephrin receptor signaling pathway / cyclin-dependent protein serine/threonine kinase activity / Schwann cell development / regulation of protein localization to plasma membrane / peptidyl-threonine phosphorylation / behavioral response to cocaine / skeletal muscle tissue development / regulation of synaptic transmission, glutamatergic / cyclin-dependent protein kinase holoenzyme complex / synapse assembly / ephrin receptor binding / negative regulation of proteolysis / NPAS4 regulates expression of target genes / positive regulation of microtubule polymerization / sensory perception of pain / negative regulation of protein ubiquitination / ionotropic glutamate receptor binding / cerebellum development / ionotropic glutamate receptor signaling pathway / axonogenesis / axon guidance / regulation of cell migration / protein serine/threonine kinase activator activity / cell-matrix adhesion / excitatory postsynaptic potential / hippocampus development / synaptic transmission, glutamatergic / filopodium / regulation of actin cytoskeleton organization / intracellular protein transport / Hsp90 protein binding / brain development / visual learning / neuromuscular junction / regulation of synaptic plasticity / tau protein binding / microtubule cytoskeleton organization / G protein-coupled acetylcholine receptor signaling pathway / neuron migration / neuron differentiation / neuron projection development / cellular response to amyloid-beta / actin filament binding / p53 binding / rhythmic process / kinase activity / positive regulation of neuron apoptotic process / cell junction / eukaryotic translation initiation factor 2alpha kinase activity / peptidyl-serine phosphorylation
Similarity search - Function
Cyclin-dependent kinase 5 activator protein / Cyclin-dependent kinase 5 activator / Cyclin-like superfamily / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Cyclin-dependent kinase 5 activator protein / Cyclin-dependent kinase 5 activator / Cyclin-like superfamily / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-65L / DI(HYDROXYETHYL)ETHER / Cyclin-dependent kinase 5 / Cyclin-dependent kinase 5 activator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsMalojcic, G. / Clugston, S.L. / Daniels, M. / Harmange, J.C. / Ledeborer, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery and Optimization of Highly Selective Inhibitors of CDK5.
Authors: Daniels, M.H. / Malojcic, G. / Clugston, S.L. / Williams, B. / Coeffet-Le Gal, M. / Pan-Zhou, X.R. / Venkatachalan, S. / Harmange, J.C. / Ledeboer, M.
History
DepositionSep 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent-like kinase 5
B: Cyclin-dependent-like kinase 5
C: Cyclin-dependent kinase 5 activator 1, p25
D: Cyclin-dependent kinase 5 activator 1, p25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,31926
Polymers113,2764
Non-polymers2,04222
Water6,702372
1
A: Cyclin-dependent-like kinase 5
C: Cyclin-dependent kinase 5 activator 1, p25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,24623
Polymers56,6382
Non-polymers1,60821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-60 kcal/mol
Surface area19390 Å2
MethodPISA
2
B: Cyclin-dependent-like kinase 5
D: Cyclin-dependent kinase 5 activator 1, p25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0733
Polymers56,6382
Non-polymers4341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-19 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.370, 118.370, 155.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSASPASPAA3 - 2883 - 288
21LYSLYSASPASPBB3 - 2883 - 288
12SERSERSERSERCC147 - 29349 - 195
22SERSERSERSERDD147 - 29349 - 195

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Cyclin-dependent-like kinase 5 / Cell division protein kinase 5


Mass: 33306.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK5, CDKN5 / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q00535, non-specific serine/threonine protein kinase
#2: Protein Cyclin-dependent kinase 5 activator 1, p25


Mass: 23331.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK5R1, CDK5R, NCK5A / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15078

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Non-polymers , 6 types, 394 molecules

#3: Chemical ChemComp-65L / [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol


Mass: 434.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23FN6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07809 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 8, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07809 Å / Relative weight: 1
ReflectionResolution: 2.09→51.79 Å / Num. obs: 74979 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.018 / Rrim(I) all: 0.081 / Net I/σ(I): 24.9 / Num. measured all: 1501558
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.09-2.1418.41.42310144855250.7820.3391.4642.4100
9.35-51.79180.0281701794710.0060.02875.899.4

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3o0g

3o0g


Resolution: 2.09→51.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.865 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 3645 4.9 %RANDOM
Rwork0.2009 ---
obs0.2022 71280 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 188.45 Å2 / Biso mean: 63.908 Å2 / Biso min: 27.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å2-0 Å2
2---0.17 Å20 Å2
3---0.56 Å2
Refinement stepCycle: final / Resolution: 2.09→51.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6820 0 131 372 7323
Biso mean--61.62 54.52 -
Num. residues----845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137095
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176824
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.6579580
X-RAY DIFFRACTIONr_angle_other_deg1.2091.5915734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16622.055365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.609151241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0561546
X-RAY DIFFRACTIONr_chiral_restr0.0660.2874
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021619
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A85960.11
12B85960.11
21C36440.17
22D36440.17
LS refinement shellResolution: 2.09→2.144 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 260 -
Rwork0.256 5252 -
all-5512 -
obs--99.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.84571.5974.11958.15452.183811.95690.1499-0.1396-0.43590.2947-0.1133-0.35580.58690.3411-0.03650.31110.04240.0310.1822-0.02360.312453.0003-47.046449.2382
23.19310.9219-0.29592.69970.41171.7711-0.0647-0.0628-0.3140.08680.0644-0.17220.23120.02490.00030.1027-0.013-0.03530.0849-0.00680.057447.4152-32.684854.072
32.309-0.02521.08631.89190.71474.574-0.0934-0.11350.09680.11260.0772-0.0012-0.165-0.08350.01620.12190.0077-0.05330.0236-0.03210.092452.8944-13.344965.7218
47.32365.27171.26577.1313-3.05274.9310.934-1.43630.22440.7649-0.39070.58040.0919-1.0587-0.54330.92770.44690.21521.45820.17851.039857.9523-44.11777.7914
56.65723.8920.02384.9812.18652.8423-0.4116-1.0873-0.85970.40290.01120.33690.4933-0.26910.40040.71080.27810.22170.91840.44960.704766.6368-52.734470.5765
64.8212-2.3003-0.78953.60580.87423.0136-0.4282-0.6686-0.20690.46250.4210.08520.31230.21660.00720.16730.1143-0.00980.3455-0.02610.160976.3641-40.069160.2775
72.007-3.5096-1.09148.3721-0.99995.01220.28320.11630.5483-0.4909-0.1689-0.9301-0.42090.298-0.11430.33830.0214-0.00830.52420.0580.367986.9281-40.401440.1393
83.29940.40010.10617.41944.00494.6085-0.1024-0.41370.87120.07390.3462-0.5637-0.4530.7022-0.24380.18490.0747-0.060.5221-0.21590.48989.2194-32.565358.9483
95.14873.28644.15318.63283.575.97290.0439-0.33790.52520.2973-0.13840.6169-0.4817-0.43860.09450.1617-0.02220.09210.3034-0.00530.136815.8839-38.134773.2412
102.1061-1.57050.77031.2047-0.77268.54590.099-0.2986-0.2111-0.0040.24380.20980.2502-0.3163-0.34280.1955-0.07840.05120.2580.06850.142712.0507-52.824369.5277
118.35551.81051.72592.48050.55770.4268-0.1564-0.299-0.04150.09990.0973-0.0273-0.0832-0.02950.05910.2906-0.0496-0.00710.27030.02980.122126.79-43.534179.7139
126.8049-3.46092.78845.5105-1.91142.64850.0007-0.15310.13210.21080.0365-0.2519-0.09960.1207-0.03720.2709-0.0681-0.0030.3012-0.00660.184735.7255-37.11478.4856
132.67392.39470.04213.3012-0.4251.19220.1-0.06130.00410.0455-0.04090.045-0.0982-0.055-0.05910.082-0.05480.00290.16160.00930.003724.7024-42.234666.9253
143.6862.39730.23838.1223-0.96473.5884-0.28760.1513-0.0715-0.38590.2501-0.6673-0.44190.47140.03760.2151-0.083-0.00980.42560.00940.225340.1054-39.037371.7298
152.44042.1932-0.35814.2972-1.22664.5536-0.1138-0.0916-0.4194-0.37720.0702-0.29010.63710.0820.04370.1125-0.04010.0180.1920.00880.088931.3891-44.187762.3615
167.32482.8602-3.69036.2691-3.53017.69630.12350.14410.6890.30770.1480.8269-0.3363-0.3732-0.27150.18050.07120.04630.212-0.01450.289417.5161-28.20865.9425
172.9615-0.02282.05390.0122-0.01541.49210.22280.4687-0.14940.06040.0577-0.07470.17650.0876-0.28051.25810.07810.12451.23540.12621.323674.1048-84.918161.538
185.9553-3.42963.43042.2613-1.8797.2326-0.1951-0.2802-1.2889-0.25130.55510.79141.3872-0.8442-0.361.4164-0.37950.07710.9482-0.12721.539268.7993-71.40750.9516
191.78471.56910.99561.9658-0.24342.85210.2596-0.0741-0.07880.04260.0224-0.02670.14150.0172-0.2820.76610.07860.10720.67340.08820.902378.0607-71.379265.397
201.8374-0.2708-0.93310.07190.13390.50170.34470.33570.6911-0.1924-0.05960.0254-0.0735-0.2851-0.28511.20180.09080.12170.96770.15921.39666.4954-73.799965.1445
215.04024.46232.7484.25652.17631.8562-0.234-0.6129-1.4544-0.55420.133-1.6105-0.0781-0.7250.1011.19290.09060.58151.1543-0.05682.456962.6957-65.357461.3121
221.40830.9717-1.68067.7050.62372.6033-0.19590.146-0.47830.54930.0654-1.10280.6746-0.09090.13050.92390.3439-0.03080.89640.34731.3180.771-68.100669.0624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 23
2X-RAY DIFFRACTION2A24 - 157
3X-RAY DIFFRACTION3A158 - 291
4X-RAY DIFFRACTION4B3 - 31
5X-RAY DIFFRACTION5B32 - 74
6X-RAY DIFFRACTION6B75 - 219
7X-RAY DIFFRACTION7B220 - 247
8X-RAY DIFFRACTION8B248 - 288
9X-RAY DIFFRACTION9C146 - 162
10X-RAY DIFFRACTION10C163 - 170
11X-RAY DIFFRACTION11C171 - 187
12X-RAY DIFFRACTION12C188 - 197
13X-RAY DIFFRACTION13C198 - 237
14X-RAY DIFFRACTION14C238 - 245
15X-RAY DIFFRACTION15C246 - 277
16X-RAY DIFFRACTION16C278 - 293
17X-RAY DIFFRACTION17D147 - 173
18X-RAY DIFFRACTION18D174 - 197
19X-RAY DIFFRACTION19D198 - 211
20X-RAY DIFFRACTION20D212 - 234
21X-RAY DIFFRACTION21D235 - 259
22X-RAY DIFFRACTION22D260 - 293

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