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

The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 61U: 5-fluoranyl-4-[[2-[(1R)-1-(1-methylpiperidin-4-yl)-1-oxidanyl-ethyl]-1,6-naphthyridin-7-yl]amino]-2-morpholin-4-yl-benzenecarbonitrile(Non-covalent)

61U.1: 19 residues within 4Å: Chain A: E.8, I.10, V.18, A.31, K.33, E.51, 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.10, A:V.18, A:A.31, A:K.33, A:V.64, A:F.80, A:F.80, A:L.133 Hydrogen bonds: A:E.51, A:C.83, A:C.83, A:D.144 Salt bridges: A:D.144

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: D.68, V.69, L.70 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.68 GOL.3: 5 residues within 4Å: Chain A: K.56, E.57 Chain B: S.172 Ligands: GOL.7, CL.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.172, B:S.172 GOL.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.5: 2 residues within 4Å: Chain A: F.286, D.288 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.286 GOL.6: 2 residues within 4Å: Chain A: E.25 Ligands: EDO.13 No protein-ligand interaction detected (PLIP) GOL.7: 6 residues within 4Å: Chain A: K.56, K.59, L.66, H.67, D.68 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.56, A:K.59, A:L.66 GOL.8: 3 residues within 4Å: Chain A: T.231, L.233, Y.236 No protein-ligand interaction detected (PLIP) GOL.28: 7 residues within 4Å: Chain B: Q.93, G.96, F.97, M.139, G.140, N.141, Y.145 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.93, B:G.96, B:M.139, B:N.141

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

EDO.9: 3 residues within 4Å: Chain A: F.82, D.84, R.136 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: N.256, A.257, R.260 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: S.119, R.120 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: V.155, R.156 Ligands: CL.41 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Ligands: GOL.6 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: H.67, D.68 Ligands: GOL.2 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: L.147, E.161, V.163, T.164 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: P.243, A.244 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: A.176, K.177, L.178, L.233 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain B: D.112, V.113, S.115 Ligands: CL.43 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: Q.90, G.91, W.92 Ligand excluded by PLIP EDO.31: 1 residues within 4Å: Ligands: CL.39 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: L.151, V.152, E.153, S.154 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain B: R.162, S.165, L.169 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain B: L.88, L.89, G.91 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain B: W.79, S.82, V.83, Q.125, L.129, P.149 Ligands: CL.44 Ligand excluded by PLIP EDO.36: 2 residues within 4Å: Chain B: A.158, R.162 Ligand excluded by PLIP

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

CL.18: 1 residues within 4Å: Chain A: G.138 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: V.272, Q.273 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain A: E.12 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain A: D.126, K.128, D.144 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain A: K.56, E.57, K.59 Ligands: GOL.3 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain A: E.28, I.29, E.81, F.82 Ligand excluded by PLIP CL.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain A: I.153, Y.158 Ligand excluded by PLIP CL.26: 1 residues within 4Å: Chain A: C.269 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain A: W.227, S.229 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain B: R.67 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain A: K.74 Chain B: K.156, E.157 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain B: R.55 Ligands: EDO.31 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain B: S.51, V.77, R.81 Ligand excluded by PLIP CL.41: 1 residues within 4Å: Ligands: EDO.12 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain B: W.92, E.142 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain B: S.116 Ligands: EDO.29 Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain B: P.149, L.151 Ligands: EDO.35 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain B: R.81, R.85 Ligand excluded by PLIP

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Cyclin-dependent-like kinase 5, p25

Cyclin-dependent kinase 5 activator 1

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