7NWK: CDK9-Cyclin T1 bound by compound 6

Crystal structure of CDK9-Cyclin T1 bound by compound 6. Determined by X-ray diffraction at 2.81 Å resolution. Released 27 Oct 2021.

Method: X-ray diffraction
Resolution: 2.81 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,435
Mol. weight: 68.36 kDa
Ligands: UT5
Released: 27 Oct 2021

Explore 7NWK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NWK 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	1
β-strand	33-38	6	1
β-strand	44-49	6	1
α-helix	61-72	12
β-strand	78	1	2
β-strand	81-86	6	1
β-strand	99-104	6	1
β-strand	108-109	2	2
α-helix	110-115	6
α-helix	123-142	20
β-strand	145-146	2	3
α-helix	152-154	3
β-strand	155-157	3	2
β-strand	163-165	3	2
β-strand	172-173	2	3
α-helix	192-194	3
α-helix	197-200	4
α-helix	209-224	16
α-helix	234-245	12
β-strand	273	1	4
α-helix	275-283	9
α-helix	286-295	10
α-helix	304-305	2
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	31-52	22
α-helix	56-69	14
α-helix	80-94	15
α-helix	101-112	12
α-helix	118-120	3
α-helix	124-143	20
α-helix	153-162	10
α-helix	168-184	17
α-helix	187-189	3
α-helix	193-208	16
α-helix	212-215	4
α-helix	221-224	4
α-helix	231-246	16
α-helix	252-255	4

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	258	Homo sapiens	O60563 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7NWK_1 Cyclin-dependent kinase 9 (chains A)
MAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFP
ITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLVK
FTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNS
QPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLAL
ISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDP
AQRIDSDDALNHDFFWSDPMPSDLKGMLST

Sequence of entity 2 (B), FASTA

>7NWK_2 Cyclin-T1 (chains B)
EGERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINT
AIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEGQPKKLEHVIKVAHTCLHPQESLPDT
RSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNS
LHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEL
LQILEKTPNRLKRIWNWR

Ligands and cofactors

ID	Name	Formula	Copies
UT5	N-((1R,3R)-3-(7-(4-fluoro-2-methoxyphenyl)-3H-imidazo[4,5-b]pyridin-2-yl)cyclop…	C20 H21 F N4 O2	1

Primary citation

Discovery of a Series of 7-Azaindoles as Potent and Highly Selective CDK9 Inhibitors for Transient Target Engagement. Barlaam, B., De Savi, C., Dishington, A. et al. J Med Chem (2021) 64:15189-15213. DOI 10.1021/acs.jmedchem.1c01249 · 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
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
4OGR 3.0 Å, crystal structure of P-TEFb complex with AFF4 and Tat

Browse structure collections

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