6W9E: Human CDK9/cyclinT1

Crystal Structure of Human CDK9/cyclinT1 in complex with MC180295. Determined by X-ray diffraction at 3.1 Å resolution. Released 1 Sept 2021.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,688
Mol. weight: 69.74 kDa
Ligands: TO7, TOJ, PO4
Released: 1 Sept 2021

Explore 6W9E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W9E contains 31 α-helices and 14 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: 16 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
α-helix	16-18	3
β-strand	19-24	6	1
β-strand	29	1	2
β-strand	31	1	2
β-strand	33-38	6	1
β-strand	44-49	6	1
α-helix	61-72	12
β-strand	78	1	3
β-strand	81-86	6	1
β-strand	99-104	6	1
α-helix	105	1
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	197-200	4
α-helix	209-224	16
α-helix	234-245	12
α-helix	275-280	6
α-helix	286-295	10
α-helix	300-302	3
α-helix	304-305	2
α-helix	306-310	5
α-helix	313-316	4
α-helix	320-321	2

Chain B: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	16-20	5
α-helix	23-26	4
α-helix	31-52	22
α-helix	56-69	14
α-helix	80-94	15
α-helix	101-112	12
α-helix	117-119	3
α-helix	124-144	21
α-helix	153-162	10
α-helix	168-184	17
α-helix	193-208	16
α-helix	212-215	4
α-helix	221-224	4
α-helix	231-247	17
α-helix	251-255	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 9	A	protein	330	Homo sapiens	P50750 (AlphaFold model)
Cyclin-T1	B	protein	259	Homo sapiens	O60563 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6W9E_1 Cyclin-dependent kinase 9 (chains A)
MAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFP
ITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLVK
FTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNS
QPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLAL
ISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDP
AQRIDSDDALNHDFFWSDPMPSDLKGMLST

Sequence of entity 2 (B), FASTA

>6W9E_2 Cyclin-T1 (chains B)
MEGERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTIN
TAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEGQPKKLEHVIKVAHTCLHPQESLPD
TRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATN
SLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHE
LLQILEKTPNRLKRIWNWR

Ligands and cofactors

ID	Name	Formula	Copies
TO7	(4-amino-2-{[(1S,2S,4R)-bicyclo[2.2.1]heptan-2-yl]amino}-1,3-thiazol-5-yl)(2-ni…	C17 H18 N4 O3 S	2
TOJ	(4-amino-2-{[(1R,2R,4S)-bicyclo[2.2.1]heptan-2-yl]amino}-1,3-thiazol-5-yl)(2-ni…	C17 H18 N4 O3 S	2
PO4	Phosphate ion	O4 P	1

Primary citation

Comparative Modeling of CDK9 Inhibitors to Explore Selectivity and Structure-Activity Relationships. Kirubakaran, P., Morton, G., Zhang, P. et al. To be published.

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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