SMTL ID : 7qhl.2 (1 other biounit)

Crystal structure of Cyclin-dependent kinase 2/cyclin A in complex with 3,5,7-Substituted pyrazolo[4,3-d]pyrimidine inhibitor 24

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x D5P: 5-(2-amino-1-ethyl)thio-3-cyclobutyl-7-[4-(pyrazol-1-yl)benzyl]amino-1(2)H-pyrazolo[4,3-d]pyrimidine(Non-covalent)

D5P.1: 14 residues within 4Å: Chain A: E.9, K.10, I.11, V.19, A.32, F.81, E.82, F.83, L.84, H.85, Q.86, D.87, Q.132, L.135 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.11, A:I.11, A:V.19, A:A.32, A:F.81, A:F.81, A:F.81, A:F.83 Hydrogen bonds: A:L.84, A:L.84, A:L.84, A:D.87, A:Q.132

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: F.5, N.24, E.29, V.31, D.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.24, A:E.29, A:E.29, A:D.69

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: K.57, L.67, L.68, D.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.70 EDO.7: 4 residues within 4Å: Chain B: H.9, R.13, K.205, T.206 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.10

2 x SGM: MONOTHIOGLYCEROL(Non-covalent)

SGM.4: 5 residues within 4Å: Chain A: E.58 Chain B: K.18, C.19, R.67, D.131 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.58, A:E.58, B:K.18 SGM.5: 2 residues within 4Å: Chain B: C.153, E.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.156, B:E.156

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 6 residues within 4Å: Chain B: M.36, I.39, L.40, W.43, L.79, Q.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jorda, R. et al., 3,5,7-Substituted Pyrazolo[4,3- d ]Pyrimidine Inhibitors of Cyclin-Dependent Kinases and Cyclin K Degraders. J.Med.Chem. (2022)

Release Date

2022-07-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Cyclin-dependent kinase 2

Cyclin-A2

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