SMTL ID : 8fp0.1

Ternary complex of CDK2 with small molecule ligands TW8672 and Roscovitine

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: S.106, Q.110, T.290, K.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.106, A:Q.110 EDO.2: 2 residues within 4Å: Chain A: T.290, K.291 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.291

1 x RRC: R-ROSCOVITINE(Non-covalent)

RRC.3: 20 residues within 4Å: Chain A: E.8, I.10, G.13, V.18, A.31, K.33, V.64, F.80, E.81, F.82, L.83, H.84, Q.85, D.86, Q.131, N.132, L.134, A.144, D.145 Ligands: 7TW.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.10, A:I.10, A:V.18, A:A.31, A:F.80, A:F.82, A:L.134, A:A.144 Hydrogen bonds: A:L.83, A:L.83, A:N.132, A:D.145

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

7TW.4: 18 residues within 4Å: Chain A: Y.15, 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 Ligands: RRC.3 17 PLIP interactions: 17 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, A:F.146 Water bridges: A:L.66 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

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