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1unl

Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and indirubin.

Method: X-RAY DIFFRACTION Dmax: 137.1 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CYCLIN-DEPENDENT KINASE 5

HOMO SAPIENS

UniProt Q00535

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 1–292 Mutation：YES CYCLIN-DEPENDENT KINASE 5 ACTIVATOR 1 × 1 （Q15078） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–292 Mutation：YES CYCLIN-DEPENDENT KINASE 5 ACTIVATOR 1 × 1 （Q15078） 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

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 1UNL 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 mutation/modification 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 mutation/modification 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 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 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 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 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
3O0G Crystal Structure of Cdk5:p25 in complex with an ATP analogue Deposited 2010-07-19 Different mutation/modification 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 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）
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 mutation/modification 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 mutation/modification 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
7VDP The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1 Deposited 2021-09-07 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 2–292（291 aa）
Not recorded 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
7VDP The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1 Deposited 2021-09-07 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 2–292（291 aa）
Not recorded 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
7VDQ The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7 Deposited 2021-09-07 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 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 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 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 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 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 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 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 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 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 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 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 1–292； UniProt 1–292 Author chain B； PDBConstruct 1–292； UniProt 1–292

CYCLIN-DEPENDENT KINASE 5 ACTIVATOR 1

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 D； UniProt 100–307 Fragment：RESIDUES 100-307 Mutation：YES CYCLIN-DEPENDENT KINASE 5 × 1 （Q00535） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 100–307 Fragment：RESIDUES 100-307 Mutation：YES CYCLIN-DEPENDENT KINASE 5 × 1 （Q00535） 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

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 1UNL 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 mutation/modification 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 mutation/modification 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 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
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 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
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 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
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 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
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
3O0G Crystal Structure of Cdk5:p25 in complex with an ATP analogue Deposited 2010-07-19 Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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
7VDP The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1 Deposited 2021-09-07 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 C 100–307（208 aa）
Not recorded 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
7VDP The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1 Deposited 2021-09-07 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 D 100–307（208 aa）
Not recorded 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
7VDQ The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7 Deposited 2021-09-07 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 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 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 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 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 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 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 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 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 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 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 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 CD5R_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 1–208； UniProt 100–307 Author chain E； PDBConstruct 1–208； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 1unl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1unl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1unl
Deposition date deposition_date2003-09-10
Structure title titleStructural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and indirubin.
Keywords keywordsCYCLIN DEPENDENT KINASE, INHIBITOR, ATP-ANALOGUE, NEURODEGENERATIVE DISEASES; CYCLIN DEPENDENT KINASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier44.90 Å
Radius of gyration Rg (electron density) rg_electron44.94 Å
Forward intensity I(0) i0143422000.00
Molecular weight molecular_weight101240.0 kDa
Excluded volume excluded_volume127750 ų
Envelope volume envelope_volume177090 ų
Hydration-shell volume shell_volume33189 ų
Envelope diameter envelope_diameter146.8 Å
Shell Rg shell_rg49.32 Å
Envelope Rg envelope_rg43.44 Å
Shape Rg shape_rg44.94 Å
Total Rg total_rg45.15 Å
Total atoms total_atoms7122
Residues n_residues884
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax137.1 Å
Rg (real space) rg_real45.30 Å
Rg uncertainty (real space) rg_real_error1.47 Å
I(0) (real space) i0_real1.4340e+08
I(0) uncertainty (real space) i0_real_error2.5180e+06
Rg (reciprocal space) rg_reciprocal44.90 Å
I(0) (reciprocal space) i0_reciprocal143400000.0000
Solution quality estimate total_estimate0.7085
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.4 Å
Skewness Skewness skewness0.298
Kurtosis Kurtosis kurtosis-0.971
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10890000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.585; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.437; Smooth: 0.016
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1unla_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd1unlb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd1unld_
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.1 — Cyclin
Domain ID domain_idd1unle_
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.1 — Cyclin

CATH v4.4 (6 domains)

Domain ID domain_id1unlA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id1unlA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id1unlB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id1unlB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id1unlD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id1unlE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
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8. Citations (1)

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9. Files and Curves (10)