SMTL ID : 8h4r.1

The Crystal Structure of CDK3 and CyclinE1 Complex with Dinaciclib from Biortus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 1QK: 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium(Non-covalent)

1QK.1: 19 residues within 4Å: Chain A: E.236, I.238, E.240, V.246, A.259, V.292, F.308, E.309, F.310, L.311, S.312, Q.313, D.314, K.317, Q.359, N.360, L.362, A.372, D.373 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.238, A:V.246, A:A.259, A:V.292, A:F.308, A:F.308, A:K.317, A:Q.359, A:L.362, A:L.362 Hydrogen bonds: A:E.236, A:L.311, A:L.311 Water bridges: A:D.373

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: S.274, R.278, T.388 Chain B: E.131, I.132 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.274, B:I.132 Water bridges: A:S.274, A:R.278, A:R.278 Salt bridges: A:R.278 SO4.4: 3 residues within 4Å: Chain A: K.284 Chain B: K.165, R.167 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:R.167 Salt bridges: B:R.167, A:K.284 SO4.5: 3 residues within 4Å: Chain B: H.275, R.277, G.278 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.278 Salt bridges: B:H.275 SO4.6: 2 residues within 4Å: Chain B: G.269, S.270 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.270 Water bridges: B:T.268 SO4.7: 4 residues within 4Å: Chain B: P.198, Q.199, Q.200 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.199, B:Q.200 Water bridges: B:I.201 SO4.8: 6 residues within 4Å: Chain B: P.195, Q.196, Y.197, Q.199, E.282, H.285 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.197, B:Y.197 Salt bridges: B:H.285

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: E.285, H.349, R.350, A.379 Chain B: K.50, S.169 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.50, B:S.169, B:S.169 Water bridges: B:K.50, B:S.169 GOL.10: 4 residues within 4Å: Chain B: Y.185, Y.197, P.198 Ligands: SO4.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.197

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.9: 1 residues within 4Å: Chain B: T.113 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gui, W. et al., The Crystal Structure of CDK3 and CyclinE1 Complex with Dinaciclib from Biortus. To Be Published

Release Date

2023-10-11

Peptides

Glutathione S-transferase class-mu 26 kDa isozyme,Cyclin-dependent kinase 3: A
G1/S-specific cyclin-E1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutathione S-transferase class-mu 26 kDa isozyme,Cyclin-dependent kinase 3

G1/S-specific cyclin-E1

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