SMTL ID : 4au8.3 (2 other biounits)

Crystal structure of compound 4a in complex with cdk5, showing an unusual binding mode to the hinge region via a water molecule

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: W.231, P.232, S.233, N.274, V.276 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.233, A:S.233, A:N.274 SO4.2: 8 residues within 4Å: Chain A: R.54, R.129, L.151, R.153, P.158, V.159, R.160, S.163 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.159, A:R.160 Salt bridges: A:R.54, A:R.129, A:R.153, A:R.160 SO4.3: 2 residues within 4Å: Chain A: F.120, R.124 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.124 SO4.5: 5 residues within 4Å: Chain B: W.231, P.232, S.233, N.274, V.276 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.233, B:S.233, B:S.233, B:N.274 SO4.6: 5 residues within 4Å: Chain B: R.54, R.129, R.153, P.158, V.159 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.159 Salt bridges: B:R.54, B:R.129, B:R.153 SO4.7: 2 residues within 4Å: Chain B: S.251, R.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.251, B:S.251 Salt bridges: B:R.264

2 x Z3R: 4-(1,3-benzothiazol-2-yl)thiophene-2-sulfonamide(Non-covalent)

Z3R.4: 13 residues within 4Å: Chain A: I.14, V.22, A.35, K.37, F.84, C.87, D.88, Q.89, D.90, K.93, L.137, A.147, D.148 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.14, A:I.14, A:V.22, A:A.35, A:F.84, A:L.137, A:L.137, A:A.147 Hydrogen bonds: A:I.14, A:D.90 Water bridges: A:D.90, A:K.93 pi-Stacking: A:F.84 Z3R.8: 12 residues within 4Å: Chain B: I.14, V.22, A.35, K.37, F.84, C.87, D.88, Q.89, D.90, K.93, L.137, D.148 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.14, B:I.14, B:V.22, B:A.35, B:L.137, B:L.137 Hydrogen bonds: B:I.14, B:D.90 Water bridges: B:K.93, B:K.93 pi-Stacking: B:F.84

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.9: 3 residues within 4Å: Chain A: Y.183 Chain B: C.57, K.60 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.60, A:Y.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malmstrom, J. et al., Synthesis and Structure-Activity Relationship of 4-(1,3-Benzothiazol-2-Yl)-Thiophene-2-Sulfonamides as Cyclin-Dependent Kinase 5 (Cdk5)/P25 Inhibitors. Bioorg.Med.Chem.Lett. (2012)

Release Date

2013-03-27

Peptides

CYCLIN-DEPENDENT KINASE 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CYCLIN-DEPENDENT KINASE 5

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