4AU8: Compound 4a

Crystal structure of compound 4a in complex with cdk5, showing an unusual binding mode to the hinge region via a water molecule. Determined by X-ray diffraction at 1.9 Å resolution. Released 27 Mar 2013.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 4,994
Mol. weight: 68.48 kDa
Ligands: Z3R
Released: 27 Mar 2013

Explore 4AU8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4AU8 contains 37 α-helices and 23 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	4-12	9	1
β-strand	17-23	7	1
β-strand	29-34	6	1
α-helix	46-55	10
β-strand	63	1	2
β-strand	66-70	5	1
β-strand	77-81	5	1
β-strand	85-86	2	2
α-helix	87-94	8
α-helix	100-119	20
β-strand	122-123	2	3
α-helix	129-131	3
β-strand	132-134	3	2
β-strand	140-142	3	2
β-strand	149-150	2	3
β-strand	153	1	3
α-helix	165-167	3
α-helix	170-173	4
α-helix	182-196	15
α-helix	208-219	12
α-helix	221-223	3
α-helix	228-232	5
α-helix	238-240	3
α-helix	242-245	4
α-helix	248-250	3
α-helix	257-266	10
α-helix	271-273	3
α-helix	275-276	2
α-helix	277-281	5
α-helix	284-286	3

Chain B: 18 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	4
β-strand	17-23	7	4
β-strand	29-36	8	4
α-helix	43-55	13
β-strand	63	1	5
β-strand	66-71	6	4
β-strand	75-80	6	4
β-strand	85-86	2	5
α-helix	87-92	6
α-helix	100-119	20
β-strand	122-123	2	6
α-helix	129-131	3
β-strand	132-134	3	5
β-strand	140-142	3	5
β-strand	149-150	2	6
α-helix	165-167	3
α-helix	170-173	4
α-helix	182-196	15
α-helix	208-219	12
α-helix	221-223	3
α-helix	228-232	5
α-helix	238-240	3
α-helix	242-245	4
α-helix	248-250	3
α-helix	257-266	10
α-helix	271-273	3
α-helix	275-276	2
α-helix	277-281	5
α-helix	284-286	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 5	A, B	protein	296	HOMO SAPIENS	Q00535 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4AU8_1 CYCLIN-DEPENDENT KINASE 5 (chains A, B)
GAMGSQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLK
ELKHKNIVRLHDVLHSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGF
CHSRNVLHRDLKPQNLLINRNGELKLADFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGA
KLYSTSIDMWSAGCIFAELANAGRPLFPGNDVDDQLKRIFRLLGTPTEEQWPSMTKLPDY
KPYPMYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAEEALQHPYFSDFCPP

Ligands and cofactors

ID	Name	Formula	Copies
Z3R	4-(1,3-benzothiazol-2-yl)thiophene-2-sulfonamide	C11 H8 N2 O2 S3	2

Water and common crystallization additives (IMD, SO4) are not listed.

Primary citation

Synthesis and Structure-Activity Relationship of 4-(1,3-Benzothiazol-2-Yl)-Thiophene-2-Sulfonamides as Cyclin-Dependent Kinase 5 (Cdk5)/P25 Inhibitors. Malmstrom, J., Viklund, J., Slivo, C. et al. Bioorg Med Chem Lett (2012) 22:5919. DOI 10.1016/J.BMCL.2012.07.068 · PubMed

Other PDB entries of the same protein (UniProt Q00535 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3O0G 1.95 Å, Crystal Structure of Cdk5:p25 in complex with an ATP analogue
7VDP 2.09 Å, The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1
9Q3N 2.1 Å, Crystal structure of human CDK5-cyclinB1 complex
1UNL 2.2 Å, Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and…
1UNG 2.3 Å, Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and…
1UNH 2.35 Å, Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and…
9Q3O 2.5 Å, Crystal structure of human CDK5-cyclinB1 complex bound to AMP-PNP
7VDR 2.55 Å, The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13
1H4L 2.65 Å, Structure and regulation of the CDK5-p25(nck5a) complex
7VDQ 2.91 Å, The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7
7VDS 3.05 Å, The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24

Browse structure collections

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