SMTL ID : 3tiy.1

CDK2 in complex with NSC 35676

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: E.28, V.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.29 EDO.2: 3 residues within 4Å: Chain A: H.84, K.89, L.298 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.84, A:K.89, A:K.89, A:L.298 EDO.3: 5 residues within 4Å: Chain A: R.126, A.149, V.154, Y.180 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.180 EDO.4: 5 residues within 4Å: Chain A: P.100, P.102, L.103, P.292, V.293 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.293 EDO.5: 7 residues within 4Å: Chain A: L.124, R.126, R.150, K.178, Y.179, Y.180 Ligands: EDO.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.126, A:R.126, A:R.150, A:K.178, A:Y.180 EDO.6: 2 residues within 4Å: Chain A: T.137, E.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.137 Water bridges: A:T.137 EDO.7: 2 residues within 4Å: Chain A: E.2, K.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.2, A:K.24 EDO.8: 7 residues within 4Å: Chain A: K.105, D.256, D.258, P.284, F.285, Q.287, D.288 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.105, A:D.256, A:D.258, A:Q.287, A:D.288 Water bridges: A:D.258, A:P.284 EDO.9: 2 residues within 4Å: Chain A: R.199, R.200 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain A: H.295, L.296, R.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.296 Water bridges: A:L.298 EDO.11: 4 residues within 4Å: Chain A: N.59, H.60, P.61, K.65 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.60 Water bridges: A:L.58, A:H.60 EDO.12: 7 residues within 4Å: Chain A: I.63, V.64, L.66, F.80, A.144, D.145, F.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.145 Water bridges: A:F.146

1 x TIY: 2,3,4,6-tetrahydroxy-5H-benzo[7]annulen-5-one(Non-covalent)

TIY.13: 12 residues within 4Å: Chain A: I.10, V.18, A.31, K.33, V.64, F.80, E.81, F.82, L.83, L.134, A.144, D.145 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.18, A:V.18, A:L.134, A:D.145 Hydrogen bonds: A:E.81, A:L.83, A:L.83, A:L.83, A:D.145 Water bridges: A:D.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martin, M.P. et al., A Novel Approach to the Discovery of Small-Molecule Ligands of CDK2. Chembiochem (2012)

Release Date

2012-08-22

Peptides

Cyclin-dependent kinase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cyclin-dependent kinase 2

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