4BCI: CDK9

Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor. Determined by X-ray diffraction at 3.1 Å resolution. Released 9 Jan 2013.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 4,597
Mol. weight: 68.57 kDa
Ligands: T3E
Released: 9 Jan 2013

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

Secondary structure: helices and β-sheets

4BCI contains 31 α-helices and 13 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: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
α-helix	16-18	3
β-strand	19-24	6	2
β-strand	33-38	6	2
β-strand	44-49	6	2
α-helix	61-72	12
β-strand	78	1	3
β-strand	81-85	5	2
β-strand	86	1	1
β-strand	100-104	5	2
β-strand	108-109	2	3
α-helix	110-115	6
α-helix	123-142	20
β-strand	145-146	2	4
α-helix	152-154	3
β-strand	155-157	3	3
β-strand	163-165	3	3
β-strand	172-173	2	4
α-helix	192-194	3
α-helix	197-200	4
α-helix	209-224	16
α-helix	234-245	12
α-helix	256-258	3
α-helix	275-280	6
α-helix	286-295	10
α-helix	306-311	6
α-helix	313-315	3
α-helix	320-321	2

Chain B: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	16-20	5
α-helix	23-26	4
α-helix	31-51	21
α-helix	56-72	17
α-helix	80-94	15
α-helix	101-112	12
α-helix	117-120	4
α-helix	124-143	20
α-helix	153-162	10
α-helix	168-184	17
α-helix	187-189	3
α-helix	193-207	15
α-helix	212-215	4
α-helix	221-224	4
α-helix	231-247	17
α-helix	252-255	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 9	A	protein	331	HOMO SAPIENS	P50750 (AlphaFold model)
Cyclin-T1	B	protein	260	HOMO SAPIENS	O60563 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4BCI_1 CYCLIN-DEPENDENT KINASE 9 (chains A)
GPAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGF
PITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLV
KFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKN
SQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLA
LISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLD
PAQRIDSDDALNHDFFWSDPMPSDLKGMLST

Sequence of entity 2 (B), FASTA

>4BCI_2 CYCLIN-T1 (chains B)
GPEGERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTI
NTAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEGQPKKLEHVIKVAHTCLHPQESLP
DTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMAT
NSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTH
ELLQILEKTPNRLKRIWNWR

Ligands and cofactors

ID	Name	Formula	Copies
T3E	3-[[5-cyano-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidin-2-yl]amino]b…	C16 H15 N7 O2 S2	1

Primary citation

Comparative Structural and Functional Studies of 4-(Thiazol- 5-Yl)-2-(Phenylamino)Pyrimidine-5-Carbonitrile Cdk9 Inhibitors Suggest the Basis for Isotype Selectivity. Hole, A.J., Baumli, S., Shao, H. et al. J Med Chem (2013) 56:660. DOI 10.1021/JM301495V · PubMed

Other PDB entries of the same protein (UniProt P50750 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MI9 2.1 Å, Crystal structure of HIV-1 Tat complexed with human P-TEFb
3BLH 2.48 Å, Crystal Structure of Human CDK9/cyclinT1
3BLR 2.8 Å, Crystal Structure of Human CDK9/cyclinT1 in complex with Flavopiridol
3MY1 2.8 Å, Structure of CDK9/cyclinT1 in complex with DRB
7NWK 2.81 Å, Crystal structure of CDK9-Cyclin T1 bound by compound 6
3BLQ 2.9 Å, Crystal Structure of Human CDK9/cyclinT1 in Complex with ATP
4OR5 2.9 Å, Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4
4IMY 2.94 Å, The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat
3TN8 2.95 Å, CDK9/cyclin T in complex with CAN508
4BCH 2.96 Å, Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine…
3LQ5 3.0 Å, Structure of CDK9/CyclinT in complex with S-CR8
3MIA 3.0 Å, Crystal structure of HIV-1 Tat complexed with ATP-bound human P-TEFb

Browse structure collections

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