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

CDK2/cyclin A2 in complex with an imidazo[1,2-c]pyrimidin-5-one inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x R7B: 8-cyclohexyl-6~{H}-imidazo[1,2-c]pyrimidin-5-one(Non-covalent)

R7B.1: 13 residues within 4Å: Chain A: I.11, E.13, G.14, V.19, A.32, V.65, F.81, E.82, F.83, L.84, Q.132, N.133, L.135 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.19 Hydrogen bonds: A:L.84, A:L.84 Water bridges: A:D.146

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

EDO.2: 3 residues within 4Å: Chain A: N.4, F.5, N.24 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.4, A:N.24 Water bridges: A:N.4, A:D.69 EDO.3: 5 residues within 4Å: Chain A: L.84, H.85, N.137, T.138, E.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.85, A:H.85 EDO.4: 8 residues within 4Å: Chain B: N.55, H.59, N.138, L.141, M.160, G.163, E.164, Y.239 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.164 EDO.5: 7 residues within 4Å: Chain B: R.37, S.166, L.167, D.169, A.170, Y.173, L.174 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.37, B:R.37, B:D.169 EDO.6: 5 residues within 4Å: Chain B: H.9, T.10, R.13, K.205, T.206 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.10 EDO.7: 4 residues within 4Å: Chain B: K.52, L.53, Q.54, K.243 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.54, B:Q.54, B:K.243

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

NA.8: 3 residues within 4Å: Chain B: M.26, Q.29, I.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.29

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.9: 3 residues within 4Å: Chain B: L.40, W.43, Q.80 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jansa, J. et al., Imidazo[1,2-c]pyrimidin-5(6H)-one inhibitors of CDK2: Synthesis, kinase inhibition and co-crystal structure. Eur.J.Med.Chem. (2021)

Release Date

2021-03-24

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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