SMTL ID : 8fow.1

Ternary complex of CDK2 with small molecule ligands TW8672 and Dinaciclib

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: L.83, H.84, N.136, T.137 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.84, A:H.84, A:T.137, A:T.137 EDO.2: 4 residues within 4Å: Chain A: S.106, Q.110, T.290, K.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.106, A:Q.110

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.3: 20 residues within 4Å: Chain A: I.10, G.11, E.12, V.18, A.31, K.33, V.64, F.80, E.81, F.82, L.83, H.84, Q.85, D.86, K.89, Q.131, N.132, L.134, A.144, D.145 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.10, A:V.18, A:A.31, A:V.64, A:F.80, A:F.80, A:F.82, A:L.134, A:A.144 Hydrogen bonds: A:K.33, A:L.83, A:L.83

1 x 7TW: 2-{[2-(1H-indol-3-yl)ethyl]amino}-5-nitrobenzoic acid(Non-covalent)

7TW.4: 16 residues within 4Å: Chain A: K.33, I.35, I.52, L.55, L.58, I.63, V.64, L.78, F.80, C.118, V.123, A.144, D.145, F.146, L.148, A.149 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.55, A:L.58, A:I.63, A:F.80, A:V.123, A:F.146, A:F.146, A:F.146, A:L.148, A:L.148 Hydrogen bonds: A:L.58, A:D.145, A:D.145, A:F.146 Salt bridges: A:K.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Faber, E.B. et al., Development of allosteric and selective CDK2 inhibitors for contraception with negative cooperativity to cyclin binding. Nat Commun (2023)

Release Date

2023-05-31

Peptides

Cyclin-dependent kinase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cyclin-dependent kinase 2

Related Entries With Identical Sequence