SAXSdb — 7vdp

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cyclin-dependent-like kinase 5

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–292	Not recorded	Cyclin-dependent kinase 5 activator 1, p25 × 1 （Q15078） 65L [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol × 1 EDO 1,2-ETHANEDIOL × 10 PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 7 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.09 Å R-free 0.229
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 2–292	Not recorded	Cyclin-dependent kinase 5 activator 1, p25 × 1 （Q15078） 65L [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.09 Å R-free 0.229

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7VDP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H4L Structure and regulation of the CDK5-p25(nck5a) complex Deposited 2001-05-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–292（292 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；MICROSEEDING - PEG3350, 100 MM TRIS PH 7.6, 200 MM KI, 10 MM DTT, PROTEIN CONC.:7 MG/ML HANGING DROP 2+2 UL. TEMPERATURE 293K.	Resolution 2.65 Å R-free 0.287
1H4L Structure and regulation of the CDK5-p25(nck5a) complex Deposited 2001-05-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–292（292 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；MICROSEEDING - PEG3350, 100 MM TRIS PH 7.6, 200 MM KI, 10 MM DTT, PROTEIN CONC.:7 MG/ML HANGING DROP 2+2 UL. TEMPERATURE 293K.	Resolution 2.65 Å R-free 0.287
1UNG Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–292（292 aa）	Mutation：YES	ALH 6-PHENYL[5H]PYRROLO[2,3-B]PYRAZINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1M KI, 0.1M BISTRISPROPANE PH 7.0, 10MM DTT	Resolution 2.30 Å R-free 0.225
1UNG Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–292（292 aa）	Mutation：YES	ALH 6-PHENYL[5H]PYRROLO[2,3-B]PYRAZINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1M KI, 0.1M BISTRISPROPANE PH 7.0, 10MM DTT	Resolution 2.30 Å R-free 0.225
1UNH Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–292（292 aa）	Mutation：YES	IXM (Z)-1H,1'H-[2,3']BIINDOLYLIDENE-3,2'-DIONE-3-OXIME × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.35 Å R-free 0.230
1UNH Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–292（292 aa）	Mutation：YES	IXM (Z)-1H,1'H-[2,3']BIINDOLYLIDENE-3,2'-DIONE-3-OXIME × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.35 Å R-free 0.230
1UNL Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–292（292 aa）	Mutation：YES	RRC R-ROSCOVITINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI, 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.20 Å R-free 0.219
1UNL Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–292（292 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI, 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.20 Å R-free 0.219
3O0G Crystal Structure of Cdk5:p25 in complex with an ATP analogue Deposited 2010-07-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–292（292 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；293 K；PEG 3350, KI, Bis-Tris Propane, pH 7, vapor diffusion, temperature 293K	Resolution 1.95 Å R-free 0.256
3O0G Crystal Structure of Cdk5:p25 in complex with an ATP analogue Deposited 2010-07-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–292（292 aa）	Not recorded	3O0 {4-amino-2-[(4-chlorophenyl)amino]-1,3-thiazol-5-yl}(3-nitrophenyl)methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；293 K；PEG 3350, KI, Bis-Tris Propane, pH 7, vapor diffusion, temperature 293K	Resolution 1.95 Å R-free 0.256
4AU8 Crystal structure of compound 4a in complex with cdk5, showing an unusual binding mode to the hinge region via a water molecule Deposited 2012-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–292（291 aa） Fragment：RESIDUES 2-292	Not recorded	SO4 SULFATE ION × 3 Z3R 4-(1,3-benzothiazol-2-yl)thiophene-2-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；pH 5.4	Resolution 1.90 Å R-free 0.234
4AU8 Crystal structure of compound 4a in complex with cdk5, showing an unusual binding mode to the hinge region via a water molecule Deposited 2012-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–292（291 aa） Fragment：RESIDUES 2-292	Not recorded	SO4 SULFATE ION × 3 Z3R 4-(1,3-benzothiazol-2-yl)thiophene-2-sulfonamide × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；pH 5.4	Resolution 1.90 Å R-free 0.234
4AU8 Crystal structure of compound 4a in complex with cdk5, showing an unusual binding mode to the hinge region via a water molecule Deposited 2012-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–292（291 aa） Fragment：RESIDUES 2-292 Chain B 2–292（291 aa） Fragment：RESIDUES 2-292	Not recorded	SO4 SULFATE ION × 6 Z3R 4-(1,3-benzothiazol-2-yl)thiophene-2-sulfonamide × 2 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；pH 5.4	Resolution 1.90 Å R-free 0.234
7VDQ The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7 Deposited 2021-09-07	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–292（291 aa）	Not recorded	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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.91 Å R-free 0.284
7VDQ The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7 Deposited 2021-09-07	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–292（291 aa）	Not recorded	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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.91 Å R-free 0.284
7VDR The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13 Deposited 2021-09-07	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–292（291 aa）	Not recorded	63I (1R)-1-[7-[(2-fluoranyl-4-pyrazol-1-yl-phenyl)amino]-1,6-naphthyridin-2-yl]-1-(1-methylpiperidin-4-yl)ethanol × 1 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 9	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.55 Å R-free 0.256
7VDR The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13 Deposited 2021-09-07	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–292（291 aa）	Not recorded	63I (1R)-1-[7-[(2-fluoranyl-4-pyrazol-1-yl-phenyl)amino]-1,6-naphthyridin-2-yl]-1-(1-methylpiperidin-4-yl)ethanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.55 Å R-free 0.256
7VDS The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24 Deposited 2021-09-07	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–292（291 aa）	Not recorded	61U 5-fluoranyl-4-[[2-[(1R)-1-(1-methylpiperidin-4-yl)-1-oxidanyl-ethyl]-1,6-naphthyridin-7-yl]amino]-2-morpholin-4-yl-benzenecarbonitrile × 1 GOL GLYCEROL × 8 EDO 1,2-ETHANEDIOL × 17 CL CHLORIDE ION × 19	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 3.05 Å R-free 0.272
7VDS The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24 Deposited 2021-09-07	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–292（291 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 3.05 Å R-free 0.272

9 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDK5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–292； UniProt 2–292 Author chain B； PDBConstruct 2–292； UniProt 2–292

Cyclin-dependent kinase 5 activator 1, p25

Homo sapiens

UniProt Q15078

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 100–307	Not recorded	Cyclin-dependent-like kinase 5 × 1 （Q00535） 65L [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol × 1 EDO 1,2-ETHANEDIOL × 10 PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 7 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.09 Å R-free 0.229
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 100–307	Not recorded	Cyclin-dependent-like kinase 5 × 1 （Q00535） 65L [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.09 Å R-free 0.229

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7VDP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H4L Structure and regulation of the CDK5-p25(nck5a) complex Deposited 2001-05-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 147–293（147 aa） Fragment：RESIDUES 147-293	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；MICROSEEDING - PEG3350, 100 MM TRIS PH 7.6, 200 MM KI, 10 MM DTT, PROTEIN CONC.:7 MG/ML HANGING DROP 2+2 UL. TEMPERATURE 293K.	Resolution 2.65 Å R-free 0.287
1H4L Structure and regulation of the CDK5-p25(nck5a) complex Deposited 2001-05-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 147–293（147 aa） Fragment：RESIDUES 147-293	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；MICROSEEDING - PEG3350, 100 MM TRIS PH 7.6, 200 MM KI, 10 MM DTT, PROTEIN CONC.:7 MG/ML HANGING DROP 2+2 UL. TEMPERATURE 293K.	Resolution 2.65 Å R-free 0.287
1UNG Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 100–307（208 aa） Fragment：RESIDUES 100-307	Not recorded	ALH 6-PHENYL[5H]PYRROLO[2,3-B]PYRAZINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1M KI, 0.1M BISTRISPROPANE PH 7.0, 10MM DTT	Resolution 2.30 Å R-free 0.225
1UNG Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 100–307（208 aa） Fragment：RESIDUES 100-307	Not recorded	ALH 6-PHENYL[5H]PYRROLO[2,3-B]PYRAZINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1M KI, 0.1M BISTRISPROPANE PH 7.0, 10MM DTT	Resolution 2.30 Å R-free 0.225
1UNH Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 100–307（208 aa） Fragment：RESIDUES 100-307	Not recorded	IXM (Z)-1H,1'H-[2,3']BIINDOLYLIDENE-3,2'-DIONE-3-OXIME × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.35 Å R-free 0.230
1UNH Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 100–307（208 aa） Fragment：RESIDUES 100-307	Not recorded	IXM (Z)-1H,1'H-[2,3']BIINDOLYLIDENE-3,2'-DIONE-3-OXIME × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.35 Å R-free 0.230
1UNL Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 100–307（208 aa） Fragment：RESIDUES 100-307	Mutation：YES	RRC R-ROSCOVITINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI, 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.20 Å R-free 0.219
1UNL Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 100–307（208 aa） Fragment：RESIDUES 100-307	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI, 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.20 Å R-free 0.219
3O0G Crystal Structure of Cdk5:p25 in complex with an ATP analogue Deposited 2010-07-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 145–293（149 aa） Fragment：UNP residues 146-293	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；293 K；PEG 3350, KI, Bis-Tris Propane, pH 7, vapor diffusion, temperature 293K	Resolution 1.95 Å R-free 0.256
3O0G Crystal Structure of Cdk5:p25 in complex with an ATP analogue Deposited 2010-07-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 145–293（149 aa） Fragment：UNP residues 146-293	Not recorded	3O0 {4-amino-2-[(4-chlorophenyl)amino]-1,3-thiazol-5-yl}(3-nitrophenyl)methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；293 K；PEG 3350, KI, Bis-Tris Propane, pH 7, vapor diffusion, temperature 293K	Resolution 1.95 Å R-free 0.256
6LDP Structure of CDK5R1-bound FEM1C Deposited 2019-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 298–307（10 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Lithium sulfate, 0.1M Tris-Hcl pH 7.9	Resolution 2.35 Å R-free 0.258
6LDP Structure of CDK5R1-bound FEM1C Deposited 2019-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 298–307（10 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Lithium sulfate, 0.1M Tris-Hcl pH 7.9	Resolution 2.35 Å R-free 0.258
7CNG Structure of CDK5R1 bound FEM1B Deposited 2020-07-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 298–307（10 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.6M Magnesium sulfate hydrate, 0.1M BIS-TRIS propane pH 6.7	Resolution 3.49 Å R-free 0.267
7CNG Structure of CDK5R1 bound FEM1B Deposited 2020-07-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 298–307（10 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.6M Magnesium sulfate hydrate, 0.1M BIS-TRIS propane pH 6.7	Resolution 3.49 Å R-free 0.267
7VDQ The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7 Deposited 2021-09-07	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 100–307（208 aa）	Not recorded	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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.91 Å R-free 0.284
7VDQ The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7 Deposited 2021-09-07	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 100–307（208 aa）	Not recorded	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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.91 Å R-free 0.284
7VDR The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13 Deposited 2021-09-07	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 100–307（208 aa）	Not recorded	63I (1R)-1-[7-[(2-fluoranyl-4-pyrazol-1-yl-phenyl)amino]-1,6-naphthyridin-2-yl]-1-(1-methylpiperidin-4-yl)ethanol × 1 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 9	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.55 Å R-free 0.256
7VDR The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13 Deposited 2021-09-07	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 100–307（208 aa）	Not recorded	63I (1R)-1-[7-[(2-fluoranyl-4-pyrazol-1-yl-phenyl)amino]-1,6-naphthyridin-2-yl]-1-(1-methylpiperidin-4-yl)ethanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.55 Å R-free 0.256
7VDS The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24 Deposited 2021-09-07	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 100–307（208 aa）	Not recorded	61U 5-fluoranyl-4-[[2-[(1R)-1-(1-methylpiperidin-4-yl)-1-oxidanyl-ethyl]-1,6-naphthyridin-7-yl]amino]-2-morpholin-4-yl-benzenecarbonitrile × 1 GOL GLYCEROL × 8 EDO 1,2-ETHANEDIOL × 17 CL CHLORIDE ION × 19	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 3.05 Å R-free 0.272
7VDS The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24 Deposited 2021-09-07	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 100–307（208 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 3.05 Å R-free 0.272

10 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD5R1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–209； UniProt 100–307 Author chain D； PDBConstruct 2–209； UniProt 100–307

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7vdp
Deposition date deposition_date	2021-09-07
Structure title title	The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1
Keywords keywords	CDK5, p25, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.29 Å
Radius of gyration Rg (electron density) rg_electron	30.36 Å
Forward intensity I(0) i0	146535000.00
Molecular weight molecular_weight	98896.0 kDa
Excluded volume excluded_volume	124930 Å³
Envelope volume envelope_volume	155160 Å³
Hydration-shell volume shell_volume	42356 Å³
Envelope diameter envelope_diameter	105.2 Å
Shell Rg shell_rg	37.69 Å
Envelope Rg envelope_rg	30.42 Å
Shape Rg shape_rg	30.34 Å
Total Rg total_rg	31.09 Å
Total atoms total_atoms	6949
Residues n_residues	845
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	100.0 Å
Rg (real space) rg_real	31.21 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	1.4650e+08
I(0) uncertainty (real space) i0_real_error	2.4240e+06
Rg (reciprocal space) rg_reciprocal	31.25 Å
I(0) (reciprocal space) i0_reciprocal	146500000.0000
Solution quality estimate total_estimate	0.8980
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.3 Å
Skewness Skewness skewness	0.282
Kurtosis Kurtosis kurtosis	-0.400
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	41270000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.939

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Cyclin-dependent-like kinase 5
Molecular weight formula_weight	33306.3 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7321

SQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKELKHKNIVRLHDVLHSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVLHRDLKPQNLLINRNGELKLADFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAKLYSTSIDMWSAGCIFAELANAGRPLFPGNDVDDQLKRIFRLLGTPTEEQWPSMTKLPDYKPYPMYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAEEALQHPYFSDFCPP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Cyclin-dependent kinase 5 activator 1, p25
Molecular weight formula_weight	23331.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MQPPPAQPPAPPASQLSGSQTGGSSSVKKAPHPAVTSAGTPKRVIVQASTSELLRCLGEFLCRRCYRLKHLSPTDPVLWLRSVDRSLLLQGWQDQGFITPANVVFLYMLCRDVISSEVGSDHELQAVLLTCLYLSYSYMGNEISYPLKPFLVESCKEAFWDRCLSVINLMSSKMLQINADPHYFTQVFSDLKNESGQEDKKRLLLGLDR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 Entity 3 non-polymer

Description description	[1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol
Molecular weight formula_weight	434.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	372

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7vdpA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	7vdpA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	7vdpB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	7vdpB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	118.370 Å
Unit-cell length b length_b	118.370 Å
Unit-cell length c length_c	155.370 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	51.790 Å
R factor r_factor	0.2022
R_work r_work	0.2009
R_free r_free	0.2287

fit	/app/data/saxs_computation/vd/7vdp/7vdp.fit
pddf	/app/data/pr_computation/vd/7vdp/7vdp.pr.out
profile	/app/data/saxs_computation/vd/7vdp/7vdp.dat

The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cyclin-dependent-like kinase 5

State in the Current Structure

Other States of the Same Protein in the Database

Cyclin-dependent kinase 5 activator 1, p25

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)