SMTL ID : 7sa0.1

Crystal structure of CDK2 liganded with compound EF4195

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: E.28, V.29, V.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.28, A:V.29 EDO.2: 9 residues within 4Å: Chain A: H.125, D.127, L.128, K.129, Q.131, N.132, L.133, A.144, D.145 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.129, A:N.132, A:N.132, A:D.145 EDO.3: 9 residues within 4Å: Chain A: L.58, N.59, H.60, P.61, I.63, V.64, K.65, L.66 Ligands: 8KQ.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.59, A:H.60 Water bridges: A:K.65, A:K.65 EDO.4: 2 residues within 4Å: Chain A: L.96, T.97 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.96

2 x 8KQ: 2-{[(3R)-2,3,4,9-tetrahydro-1H-carbazol-3-yl]amino}-5-(trifluoromethyl)benzoic acid(Non-covalent)

8KQ.5: 18 residues within 4Å: Chain A: I.10, V.18, K.20, A.31, K.33, V.64, F.80, E.81, F.82, L.83, H.84, Q.85, D.86, K.89, N.132, L.134, A.144, D.145 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.10, A:V.18, A:A.31, A:F.82, A:D.86, A:N.132, A:L.134, A:L.134 Hydrogen bonds: A:L.83, A:L.83 8KQ.6: 24 residues within 4Å: Chain A: Y.15, K.33, I.35, I.52, L.55, L.58, I.63, V.64, K.65, L.66, L.76, L.78, F.80, F.117, C.118, H.121, V.123, D.145, F.146, L.148, A.149, F.152, V.154 Ligands: EDO.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.55, A:L.58, A:L.58, A:I.63, A:L.66, A:L.78, A:F.80, A:F.117, A:V.123, A:V.123, A:F.146, A:L.148, A:L.148 Hydrogen bonds: A:L.55, A:D.145, A:F.146 Salt bridges: A:K.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, L. et al., Development of selective allosteric inhibitors of cyclin-dependent kinase 2 (CDK2). To Be Published

Release Date

2022-10-05

Peptides

Cyclin-dependent kinase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cyclin-dependent kinase 2

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