SMTL ID : 7vdp.1 (1 other biounit)

The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 65L: [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol(Non-covalent)

65L.1: 20 residues within 4Å: Chain A: I.10, E.12, V.18, A.31, K.33, V.64, F.80, E.81, F.82, C.83, D.84, Q.85, D.86, K.89, Q.130, N.131, L.133, D.144 Ligands: EDO.2, CL.12 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.10, A:A.31, A:V.64, A:F.80, A:F.80, A:K.89, A:L.133 Hydrogen bonds: A:C.83, A:C.83, A:D.144 Water bridges: A:K.33

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

EDO.2: 4 residues within 4Å: Chain A: I.10, D.86, Q.130 Ligands: 65L.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.86, A:D.86 EDO.3: 3 residues within 4Å: Chain A: H.60, K.61, R.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.65 EDO.4: 4 residues within 4Å: Chain A: V.272, Q.273, R.274, E.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.274 EDO.5: 4 residues within 4Å: Chain A: K.104, S.105, F.108, F.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.286 Water bridges: A:S.105, A:S.105 EDO.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain A: Q.85, Y.90, I.134, N.135, R.136, G.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.85, A:R.136 EDO.8: 3 residues within 4Å: Chain A: E.57 Chain B: S.171 Ligands: PEG.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.171 Water bridges: B:S.172 EDO.18: 4 residues within 4Å: Chain B: S.172, L.175, Q.176, A.179 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.172, B:Q.176 EDO.19: 4 residues within 4Å: Chain B: E.117, V.118, G.119, E.123 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.119 EDO.20: 3 residues within 4Å: Chain B: S.51, E.52, R.55 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.52, B:E.52 Water bridges: B:R.55

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 6 residues within 4Å: Chain A: K.56, K.59, L.66, H.67, D.68 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.56, A:K.56, A:K.59 PEG.10: 7 residues within 4Å: Chain A: S.247, L.248, V.249, A.257, R.260, D.261, Q.264 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.247, A:L.248, A:V.249, A:A.257, A:R.260 Water bridges: A:D.261

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 2 residues within 4Å: Chain A: K.213, K.237 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain A: E.51, V.64, F.80, A.143, D.144 Ligands: 65L.1 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: Y.4, N.23, V.30 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: K.268, C.269 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: Y.236, Y.239 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: G.138 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: R.67, K.69 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 5 residues within 4Å: Chain A: T.17, F.19, R.34, R.36, K.75 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.6, A:T.17, A:R.36, A:R.36, A:K.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Daniels, M.H. et al., Discovery and Optimization of Highly Selective Inhibitors of CDK5. J.Med.Chem. (2022)

Release Date

2022-03-09

Peptides

Cyclin-dependent-like kinase 5: A
Cyclin-dependent kinase 5 activator 1, p25: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Cyclin-dependent-like kinase 5

Cyclin-dependent kinase 5 activator 1, p25

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