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

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Basic information

Entry
Database: PDB / ID: 7vdr
TitleThe structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13
Components
  • Cyclin-dependent kinase 5 activator 1, p25
  • Cyclin-dependent-like kinase 5
KeywordsTRANSFERASE / CDK5 / p25
Function / homology
Function and homology information


positive regulation of presynaptic cytosolic calcium concentration / negative regulation of calcium ion-dependent exocytosis of neurotransmitter / 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 ...positive regulation of presynaptic cytosolic calcium concentration / negative regulation of calcium ion-dependent exocytosis of neurotransmitter / 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 / negative regulation of axon extension / layer formation in cerebral cortex / neuron cell-cell adhesion / positive regulation of calcium ion-dependent exocytosis / corpus callosum development / receptor catabolic process / cerebellar cortex formation / protein localization to synapse / CRMPs in Sema3A signaling / regulation of dendritic spine morphogenesis / NGF-stimulated transcription / ErbB-3 class receptor binding / synaptic transmission, dopaminergic / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of protein export from nucleus / motor neuron axon guidance / cyclin-dependent protein serine/threonine kinase activator activity / axonal fasciculation / axon extension / calcium ion import / regulation of neuron differentiation / regulation of synaptic vesicle recycling / tau-protein kinase activity / dendrite morphogenesis / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / receptor clustering / synaptic vesicle transport / central nervous system neuron development / negative regulation of cell cycle / oligodendrocyte differentiation / peptidyl-threonine phosphorylation / synaptic vesicle exocytosis / DARPP-32 events / positive regulation of protein targeting to membrane / synaptic vesicle endocytosis / regulation of macroautophagy / protein kinase activator activity / ephrin receptor signaling pathway / cyclin-dependent protein serine/threonine kinase activity / alpha-tubulin binding / Schwann cell development / regulation of synaptic transmission, glutamatergic / beta-tubulin binding / regulation of protein localization to plasma membrane / skeletal muscle tissue development / cyclin-dependent protein kinase holoenzyme complex / synapse assembly / behavioral response to cocaine / NPAS4 regulates expression of target genes / negative regulation of proteolysis / positive regulation of microtubule polymerization / negative regulation of protein ubiquitination / ionotropic glutamate receptor binding / sensory perception of pain / ionotropic glutamate receptor signaling pathway / axonogenesis / axon guidance / regulation of cell migration / cerebellum development / cell-matrix adhesion / protein serine/threonine kinase activator activity / regulation of actin cytoskeleton organization / excitatory postsynaptic potential / synaptic transmission, glutamatergic / filopodium / hippocampus development / neuromuscular junction / intracellular protein transport / Hsp90 protein binding / brain development / peptidyl-serine phosphorylation / regulation of synaptic plasticity / visual learning / microtubule cytoskeleton organization / tau protein binding / neuron migration / cellular response to amyloid-beta / G protein-coupled acetylcholine receptor signaling pathway / neuron differentiation / neuron projection development / actin filament binding / p53 binding / kinase activity / cell junction / rhythmic process / positive regulation of neuron apoptotic process / presynapse / lamellipodium / Factors involved in megakaryocyte development and platelet production
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-63I / TRIETHYLENE GLYCOL / Cyclin-dependent kinase 5 / Cyclin-dependent kinase 5 activator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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)114,87816
Polymers113,2764
Non-polymers1,60212
Water1,24369
1
A: Cyclin-dependent-like kinase 5
C: Cyclin-dependent kinase 5 activator 1, p25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,79413
Polymers56,6382
Non-polymers1,15511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-6 kcal/mol
Surface area19670 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)57,0853
Polymers56,6382
Non-polymers4471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-18 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.830, 117.830, 154.930
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
12SERSERGLUGLUCC147 - 29249 - 194
22SERSERGLUGLUDD147 - 29249 - 194

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 , 4 types, 81 molecules

#3: Chemical ChemComp-63I / (1R)-1-[7-[(2-fluoranyl-4-pyrazol-1-yl-phenyl)amino]-1,6-naphthyridin-2-yl]-1-(1-methylpiperidin-4-yl)ethanol


Mass: 446.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H27FN6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 291 K / Method: evaporation / 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: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920126 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920126 Å / Relative weight: 1
ReflectionResolution: 2.55→29.65 Å / Num. obs: 41128 / % possible obs: 99.9 % / Redundancy: 20.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.033 / Rrim(I) all: 0.149 / Net I/σ(I): 18.4 / Num. measured all: 855062
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
2.55-2.6521.81.8539973745810.7140.4061.8972.2100
9.19-29.6519.40.053183499480.9990.0120.05552.597.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O0G

3o0g


Resolution: 2.55→29.65 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.918 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.454 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 1980 4.8 %RANDOM
Rwork0.2188 ---
obs0.2206 39112 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 184.96 Å2 / Biso mean: 78.045 Å2 / Biso min: 31.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.24 Å20 Å2
2--0.49 Å2-0 Å2
3----1.58 Å2
Refinement stepCycle: final / Resolution: 2.55→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6849 0 112 69 7030
Biso mean--73.79 51.17 -
Num. residues----849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137117
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176835
X-RAY DIFFRACTIONr_angle_refined_deg1.321.6589622
X-RAY DIFFRACTIONr_angle_other_deg1.1251.5915758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3065841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97522.049366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.062151245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6771546
X-RAY DIFFRACTIONr_chiral_restr0.0560.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027848
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021630
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A85660.09
12B85660.09
21C39000.14
22D39000.14
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 153 -
Rwork0.31 2874 -
all-3027 -
obs--100 %
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)
111.0949-1.49776.37066.93335.308711.45040.232-0.6433-0.21610.7561-0.2369-0.2010.70990.19630.00490.4568-0.11330.02540.43820.04430.414152.6914-46.436351.958
23.26240.6505-0.30032.8340.32232.11-0.0398-0.0525-0.35040.05280.0604-0.22520.26790.148-0.02060.0857-0.0046-0.03930.0833-0.02090.09547.3425-33.10353.6487
33.09370.26221.03842.17250.46444.5688-0.1176-0.06420.05430.09990.1114-0.1014-0.22190.04050.00620.10160.0073-0.05290.0221-0.04320.123152.5322-13.089765.5356
42.94020.40780.3144.933-1.30613.5556-0.2716-1.255-0.24270.69450.01790.46630.2718-0.47350.25370.73480.18520.13271.2550.22580.761160.9861-48.358473.6964
52.9681-2.03590.05061.49150.00440.343-0.0897-0.7584-0.74880.24290.24870.5151-0.0889-0.2951-0.1590.9238-0.01090.09331.31090.2230.585266.9394-50.044174.5939
64.4832-2.85760.29656.3314-1.46885.3562-0.3719-0.91880.47260.71940.5623-0.2293-0.25530.0449-0.19040.28310.1226-0.05540.5977-0.17850.319769.2779-28.443567.4795
74.8998-0.3997-0.15936.6649-0.00762.3796-0.3132-0.7929-0.18420.5510.2782-0.16740.29880.14270.0350.29210.2056-0.00260.6551-0.02440.279678.308-42.280566.0352
83.9543-3.134-0.67483.49570.65973.2466-0.1589-0.2646-0.12560.16730.282-0.0130.27940.1604-0.12310.09220.04420.00150.3182-0.06340.24977.3419-40.070453.0516
97.6409-3.95890.9095.01650.27741.28910.2511.12910.5977-0.3215-0.4009-0.6067-0.21810.34710.14990.21460.03090.03930.42890.00110.261482.832-36.96642.6718
101.5116-2.3727-0.779110.5555-1.32571.35520.2356-0.01120.13380.2582-0.258-0.411-0.33310.11170.02240.3622-0.01620.00770.4336-0.01890.30384.2698-39.720439.1441
119.25972.2306-0.992514.10670.43470.4614-0.11370.13611.1561-0.22990.2847-0.3165-0.4040.0869-0.1710.5379-0.0201-0.00130.5277-0.20950.611286.9503-26.153556.9949
126.45244.15512.769310.85694.45022.116-0.3138-0.09410.63360.80820.2156-0.24550.18140.27790.09820.1902-0.0005-0.08351.014-0.08840.518190.4355-37.40360.1075
136.25243.50753.32165.62472.08995.87270.2377-0.62410.73950.7542-0.53541.1535-0.3192-0.65090.29770.2409-0.05570.14010.3002-0.05370.259615.7188-37.87673.0837
140.19210.161.10290.1510.91636.46140.1797-0.1196-0.03170.152-0.01410.02870.634-0.529-0.16560.4041-0.14610.06360.47150.06260.248912.291-51.262970.846
1510.84241.94973.05324.69420.29011.37890.1486-0.55530.01270.4795-0.2056-0.14820.0624-0.06770.0570.264-0.0820.0010.27490.04860.068728.0109-42.957479.6393
166.1016-1.676-1.94972.0133-0.19810.99820.2230.13310.28840.2178-0.278-0.4211-0.13120.1210.05510.3029-0.0383-0.06380.37280.0160.245735.4569-36.701778.2613
171.96242.78160.73593.99051.3312.00780.09780.01150.06750.09270.00450.0721-0.2221-0.078-0.10240.0656-0.04060.00790.1749-0.01590.094621.2538-39.60365.4656
184.87774.5806-2.77356.5578-3.11052.5504-0.0144-0.1883-0.07510.08770.0503-0.01850.08590.0242-0.03590.0937-0.0549-0.05390.13730.02170.051827.9013-44.360868.0865
197.18212.25841.602713.164-0.0633.519-0.03440.0523-0.5422-0.01040.1836-1.3453-0.09370.3926-0.14920.1387-0.0571-0.00880.34660.05620.178936.5432-45.531171.3026
203.00912.182-0.81128.8749-2.52174.4738-0.1184-0.0527-0.1515-0.81980.1262-0.46470.54620.0485-0.00780.1187-0.04380.02930.1212-0.02180.044430.4285-41.306559.1584
2111.48082.3714-3.64584.2112-0.12725.18550.30690.33210.49280.65330.1060.7116-0.7818-0.8482-0.4130.320.12790.12160.24020.04450.309317.172-27.929265.7434
220.02410.07810.1270.27170.43510.71230.04760.0009-0.07290.20360.1393-0.16270.39580.1282-0.18691.39860.05460.1521.1640.23131.875671.1037-80.02658.1445
234.91060.74530.97713.6593-3.94510.0444-0.26440.0812-0.6957-0.2957-0.1085-0.27350.52630.63610.37290.840.08390.1190.5292-0.01051.195174.6643-68.437658.0141
241.40071.16672.53370.9722.10814.76180.3058-0.46930.09660.2437-0.39820.05891.0051-0.78880.09251.30950.18550.2190.78250.36111.704267.1167-72.417965.735
250.14570.46280.49422.86321.41562.7147-0.0046-0.0755-0.28090.1370.1297-0.23840.6255-0.2816-0.12521.09890.26970.27591.11140.5641.817172.5606-66.739766.0109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 16
2X-RAY DIFFRACTION2A17 - 157
3X-RAY DIFFRACTION3A158 - 291
4X-RAY DIFFRACTION4B3 - 57
5X-RAY DIFFRACTION5B58 - 81
6X-RAY DIFFRACTION6B82 - 99
7X-RAY DIFFRACTION7B100 - 157
8X-RAY DIFFRACTION8B158 - 207
9X-RAY DIFFRACTION9B208 - 229
10X-RAY DIFFRACTION10B230 - 247
11X-RAY DIFFRACTION11B248 - 266
12X-RAY DIFFRACTION12B267 - 288
13X-RAY DIFFRACTION13C146 - 162
14X-RAY DIFFRACTION14C163 - 172
15X-RAY DIFFRACTION15C173 - 187
16X-RAY DIFFRACTION16C188 - 197
17X-RAY DIFFRACTION17C198 - 218
18X-RAY DIFFRACTION18C219 - 237
19X-RAY DIFFRACTION19C238 - 253
20X-RAY DIFFRACTION20C254 - 277
21X-RAY DIFFRACTION21C278 - 293
22X-RAY DIFFRACTION22D147 - 187
23X-RAY DIFFRACTION23D188 - 209
24X-RAY DIFFRACTION24D210 - 237
25X-RAY DIFFRACTION25D238 - 293

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