SMTL ID : 9gla.1

Crystal structure of a CDK2-based CDK7 mimic with inhibitor SY5609

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

hetero-1-1-mer

Ligands

1 x YNK: 7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile(Non-covalent)

YNK.1: 18 residues within 4Å: Chain A: L.10, G.11, E.12, V.18, A.31, I.64, F.80, E.81, F.82, M.83, E.84, T.85, D.86, V.89, N.132, L.134, A.144, D.145 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.10, A:V.18, A:A.31, A:V.89, A:L.134 Hydrogen bonds: A:M.83, A:M.83, A:D.86, A:D.145 Halogen bonds: A:E.81

1 x SGM: MONOTHIOGLYCEROL(Non-covalent)

SGM.2: 6 residues within 4Å: Chain A: E.57 Chain B: M.15, K.18, C.19, R.67, D.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.18

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: V.154 Chain B: H.5, Q.143, L.146, H.147, K.205 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.147, B:K.205 NA.4: 3 residues within 4Å: Chain B: M.26, Q.29, I.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skerlova, J. et al., CDK2-based CDK7 mimic as a tool for structural analysis: Biochemical validation and crystal structure with SY5609. Int.J.Biol.Macromol. (2025)

Release Date

2025-04-02

Peptides

Cyclin-dependent kinase 2: A
Cyclin-A2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cyclin-dependent kinase 2

Cyclin-A2

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