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

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Basic information

Entry
Database: PDB / ID: 7vdq
TitleThe structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7
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 / protein kinase 5 complex / acetylcholine receptor activator activity / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / Activated NTRK2 signals through CDK5 / layer formation in cerebral cortex / neuron cell-cell adhesion ...superior olivary nucleus maturation / protein kinase 5 complex / acetylcholine receptor activator activity / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / Activated NTRK2 signals through CDK5 / layer formation in cerebral cortex / neuron cell-cell adhesion / positive regulation of calcium ion-dependent exocytosis / negative regulation of axon extension / receptor catabolic process / regulation of synaptic vesicle cycle / protein localization to synapse / corpus callosum development / regulation of dendritic spine morphogenesis / cerebellar cortex formation / CRMPs in Sema3A signaling / NGF-stimulated transcription / synaptic transmission, dopaminergic / ErbB-3 class receptor binding / calcium ion import / negative regulation of protein export from nucleus / axon extension / cyclin-dependent protein serine/threonine kinase activator activity / regulation of synaptic vesicle recycling / axonal fasciculation / motor neuron axon guidance / dendrite morphogenesis / embryo development ending in birth or egg hatching / regulation of neuron differentiation / synaptic vesicle transport / regulation of cyclin-dependent protein serine/threonine kinase activity / tau-protein kinase activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / beta-tubulin binding / protein kinase activator activity / central nervous system neuron development / oligodendrocyte differentiation / receptor clustering / synaptic vesicle exocytosis / behavioral response to cocaine / synaptic vesicle endocytosis / negative regulation of cell cycle / DARPP-32 events / alpha-tubulin binding / cyclin-dependent protein kinase holoenzyme complex / positive regulation of protein targeting to membrane / ephrin receptor signaling pathway / regulation of protein localization to plasma membrane / regulation of macroautophagy / cyclin-dependent protein serine/threonine kinase activity / Schwann cell development / skeletal muscle tissue development / regulation of synaptic transmission, glutamatergic / regulation of cell migration / sensory perception of pain / positive regulation of microtubule polymerization / negative regulation of protein ubiquitination / synapse assembly / NPAS4 regulates expression of target genes / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / ephrin receptor binding / protein serine/threonine kinase activator activity / cerebellum development / axonogenesis / cell-matrix adhesion / filopodium / synaptic transmission, glutamatergic / hippocampus development / negative regulation of proteolysis / regulation of actin cytoskeleton organization / peptidyl-threonine phosphorylation / axon guidance / intracellular protein transport / ionotropic glutamate receptor binding / neuron migration / Hsp90 protein binding / visual learning / regulation of synaptic plasticity / tau protein binding / neuromuscular junction / neuron differentiation / G protein-coupled acetylcholine receptor signaling pathway / brain development / microtubule cytoskeleton organization / cellular response to amyloid-beta / neuron projection development / actin filament binding / positive regulation of neuron apoptotic process / rhythmic process / p53 binding / presynapse / cell junction / lamellipodium / kinase activity / Factors involved in megakaryocyte development and platelet production / growth cone
Similarity search - Function
Cyclin-dependent kinase 5 activator / Cyclin-dependent kinase 5 activator protein / Cyclin-like superfamily / 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. ...Cyclin-dependent kinase 5 activator / Cyclin-dependent kinase 5 activator protein / Cyclin-like superfamily / 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
Similarity search - Domain/homology
Chem-64V / Cyclin-dependent kinase 5 / Cyclin-dependent kinase 5 activator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 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)114,2886
Polymers113,2764
Non-polymers1,0112
Water1267
1
A: Cyclin-dependent-like kinase 5
C: Cyclin-dependent kinase 5 activator 1, p25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1443
Polymers56,6382
Non-polymers5061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-17 kcal/mol
Surface area19220 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)57,1443
Polymers56,6382
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-18 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.610, 117.610, 154.010
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
11LYSLYSSERSERAA3 - 2873 - 287
21LYSLYSSERSERBB3 - 2873 - 287
12SERSERGLUGLUCC147 - 29249 - 194
22SERSERGLUGLUDD147 - 29249 - 194

NCS ensembles :
ID
1
2

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Components

#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 / p25 / Tau protein kinase II 23 kDa subunit / p23


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
#3: Chemical ChemComp-64V / 2-[[7-[[2-fluoranyl-4-[3-(hydroxymethyl)pyrazol-1-yl]phenyl]amino]-1,6-naphthyridin-2-yl]-(1-methylpiperidin-4-yl)amino]ethanoic acid


Mass: 505.544 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H28FN7O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.69 %
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: 1.12709 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 21, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 2.91→38.67 Å / Num. obs: 27572 / % possible obs: 99.9 % / Redundancy: 19.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.039 / Rrim(I) all: 0.173 / Net I/σ(I): 15.5 / Num. measured all: 548565
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
2.91-2.9921.11.7864212519950.690.3941.832.1100
13.01-38.6714.60.06449743400.9970.0160.06637.895.7

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O0G

3o0g


Resolution: 2.91→38.5 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.888 / SU B: 42.476 / SU ML: 0.376 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2839 1392 5.1 %RANDOM
Rwork0.2523 ---
obs0.2539 26146 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 221.21 Å2 / Biso mean: 89.173 Å2 / Biso min: 38.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.14 Å2-0 Å2
2---0.29 Å20 Å2
3---0.93 Å2
Refinement stepCycle: final / Resolution: 2.91→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6865 0 74 7 6946
Biso mean--80.39 54.89 -
Num. residues----851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137106
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176769
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.6569630
X-RAY DIFFRACTIONr_angle_other_deg1.0871.59115617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35422.135370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.647151244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9141546
X-RAY DIFFRACTIONr_chiral_restr0.0540.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021631
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A83850.12
12B83850.12
21C38110.15
22D38110.15
LS refinement shellResolution: 2.91→2.985 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 95 -
Rwork0.31 1884 -
all-1979 -
obs--99.9 %
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)
13.9395-0.25131.86523.72683.56638.84950.1294-0.0196-0.17850.3183-0.1508-0.17220.20740.50210.02150.3175-0.0515-0.00980.3254-0.04990.319953.0183-46.394250.2545
24.5933-1.6736-2.56815.06542.09526.34350.0672-0.4441-0.54280.47060.1858-0.21970.47470.4482-0.25290.2148-0.1195-0.08230.2938-0.04510.189844.1264-43.517155.6474
31.69850.0103-1.65038.7984-2.48653.9028-0.14080.2284-0.4129-0.17420.0046-0.2880.1751-0.26910.13620.1966-0.0907-0.03040.2935-0.04960.217442.7977-40.003950.807
43.7169-0.2204-0.12463.56111.66521.161-0.20120.54220.0879-0.2630.2675-0.30990.02590.304-0.06630.2918-0.07070.01040.30350.06530.059555.4935-22.892349.1886
59.13080.6335-4.29184.98080.91745.40160.2902-0.0259-0.31770.0096-0.037-0.29380.36290.3261-0.25320.1998-0.0083-0.09430.09380.00860.092949.2886-27.543153.5615
63.13431.6063.24182.71281.81593.3660.1806-0.5661-0.14520.5878-0.06510.21530.2229-0.5703-0.11550.3309-0.04890.02680.29180.02510.205843.9355-24.125266.7556
73.3869-0.56231.73542.8097-0.12336.32730.1054-0.0211-0.27040.23730.1852-0.35950.18370.3734-0.29060.1871-0.0158-0.03190.1117-0.02160.091157.0825-17.025165.2746
88.23983.4239-1.66917.9417-1.66022.4816-0.1104-0.21930.41740.19550.03480.428-0.4285-0.30050.07560.3780.028-0.07090.2719-0.05710.057650.8438-7.50175.8649
96.79293.77361.07974.3794-3.79138.7669-0.29350.37850.0565-0.22210.0844-0.13570.01270.50630.20910.4038-0.0635-0.02830.3234-0.09990.212458.763-8.222155.366
104.32810.8608-0.61492.9902-1.80666.96260.00980.38070.3704-0.1340.18930.1174-0.4594-0.2577-0.19910.2760.0004-0.04430.1717-0.00230.273747.225-9.287953.9593
111.47141.3094-0.13756.6282-1.78990.5347-0.0028-0.51170.49161.0933-0.00250.4444-0.2575-0.08820.00520.81280.23850.12761.2942-0.01120.7560.9061-49.377872.8838
122.6432-2.44170.95875.40261.09841.69890.0297-0.17410.00840.696-0.12420.01870.23-0.26410.09450.76690.09060.02070.9624-0.10470.46973.0692-39.824269.8298
130.81990.1928-0.80163.0535-2.11215.4065-0.2708-0.2987-0.0950.39060.29260.09760.24460.295-0.02190.30460.09780.01710.5975-0.12520.514578.127-46.017156.2213
142.7836-3.8621-0.94815.38161.15573.84980.40040.15410.5095-0.5716-0.3348-0.7173-0.57340.1735-0.06550.5956-0.03060.05780.8193-0.03740.618381.3199-36.56743.3518
153.53811.2465-0.25611.33594.56792.06240.15330.20880.5549-0.0304-0.17540.3199-0.15310.05470.02210.6478-0.05930.03470.8658-0.12790.659788.7871-32.159458.6069
165.72365.4496.67089.92337.28718.0238-0.3124-0.60410.60320.7356-0.44811.507-0.1135-0.59980.76050.4141-0.07450.09030.4846-0.12880.469515.6815-37.935372.6571
177.342-2.3481-2.84215.12837.831512.38960.5821-0.6067-0.0579-0.1411-0.03960.0084-0.4114-0.1776-0.54250.3774-0.02880.34320.37050.12650.874712.0113-52.726468.965
188.90510.47433.21562.6930.87721.4570.0453-0.0837-0.04880.5148-0.07160.1470.02960.14920.02640.4361-0.10690.03080.44040.01350.063526.7192-43.034379.1981
1912.4071-7.98211.20396.57981.25023.12620.063-0.1160.47390.1760.2146-0.5374-0.00780.3839-0.27760.6281-0.26970.00420.58470.05540.176735.3896-36.597477.9286
200.3683-0.70980.02276.01292.09491.0605-0.0132-0.07380.05720.2545-0.35770.8107-0.018-0.25950.37090.2731-0.1080.11390.3491-0.04250.243521.302-39.69764.9999
216.02476.302-3.105212.6233-6.35174.7571-0.08940.1527-0.02930.25290.3846-0.07130.00410.0172-0.29520.1949-0.0205-0.04130.3008-0.04720.071427.9612-44.36767.7674
223.7816-0.00740.27896.0448-0.79130.553-0.27050.2525-0.38250.41420.3624-0.82910.050.3007-0.09190.3095-0.009-0.07740.5473-0.09280.288436.6263-45.528671.1311
234.51194.2997-0.59914.5393-2.01324.8185-0.32610.1456-0.2464-0.43990.0997-0.28430.38930.09640.22630.1965-0.0161-0.01330.2713-0.04520.043530.5647-41.461758.8883
246.67525.2054-4.86257.2163-4.10188.5828-0.00780.10160.3460.120.19820.4518-0.4456-0.4445-0.19040.33650.05750.06970.2561-0.04520.379517.1257-28.009565.1602
250.6025-1.77172.847610.5792-14.924921.5079-0.04110.00410.16280.22890.02810.2469-0.3434-0.16260.0130.60530.0051-0.03820.71190.03470.723780.635-79.564556.2344
262.49740.04161.19480.01440.01370.6797-0.01860.0259-0.31470.01240.0507-0.09710.3114-0.0545-0.03211.0253-0.12310.12950.5928-0.07390.938969.367-87.226866.4098
271.18310.89371.59330.85871.60323.04480.0527-0.1686-0.84340.2031-0.05-0.12830.5746-0.1534-0.00281.25990.04410.40950.90440.08762.08268.4586-71.27851.4579
281.94351.15141.99062.19884.651910.06980.2290.11030.1353-0.20310.1085-0.1031-0.38260.3508-0.33750.61280.07910.03890.55970.04920.612378.177-70.629763.3614
290.1349-0.2114-0.48193.35181.31992.3294-0.03310.0123-0.06290.9783-0.25341.54351.0080.09740.28651.26990.12230.16581.05240.44541.678567.6951-72.690666.0399
300.1126-0.5427-0.08194.68750.87274.0381-0.15-0.1539-0.27620.35350.63210.34630.4953-0.2843-0.48210.94650.18590.17841.09280.381.297672.5779-66.887866.0916
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 23
2X-RAY DIFFRACTION2A24 - 57
3X-RAY DIFFRACTION3A58 - 81
4X-RAY DIFFRACTION4A82 - 119
5X-RAY DIFFRACTION5A120 - 139
6X-RAY DIFFRACTION6A140 - 180
7X-RAY DIFFRACTION7A181 - 219
8X-RAY DIFFRACTION8A220 - 247
9X-RAY DIFFRACTION9A248 - 266
10X-RAY DIFFRACTION10A267 - 291
11X-RAY DIFFRACTION11B3 - 57
12X-RAY DIFFRACTION12B58 - 139
13X-RAY DIFFRACTION13B140 - 195
14X-RAY DIFFRACTION14B196 - 247
15X-RAY DIFFRACTION15B248 - 288
16X-RAY DIFFRACTION16C146 - 162
17X-RAY DIFFRACTION17C163 - 170
18X-RAY DIFFRACTION18C171 - 187
19X-RAY DIFFRACTION19C188 - 197
20X-RAY DIFFRACTION20C198 - 218
21X-RAY DIFFRACTION21C219 - 237
22X-RAY DIFFRACTION22C238 - 253
23X-RAY DIFFRACTION23C254 - 277
24X-RAY DIFFRACTION24C278 - 293
25X-RAY DIFFRACTION25D147 - 154
26X-RAY DIFFRACTION26D155 - 173
27X-RAY DIFFRACTION27D174 - 197
28X-RAY DIFFRACTION28D198 - 208
29X-RAY DIFFRACTION29D209 - 237
30X-RAY DIFFRACTION30D238 - 293

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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