SMTL ID : 9epu.1

Crystal structure of the human CDKL5 kinase domain with compound CAF-382

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x 01: ~{N}-[5-[(5-propan-2-yl-1,3-oxazol-2-yl)methylsulfanyl]-1,3-thiazol-2-yl]piperidine-4-carboxamide

01.1: 21 residues within 4Å: Chain A: V.20, G.21, Y.25, V.28, A.41, K.43, V.74, F.90, E.91, Y.92, V.93, E.94, K.95, N.96, E.99, E.140, N.141, L.143, C.153, D.154 Chain B: E.102 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.20, A:Y.25 Hydrogen bonds: A:V.93, A:V.93 01.6: 21 residues within 4Å: Chain A: E.102 Chain B: V.20, G.21, Y.25, V.28, A.41, K.43, V.74, F.90, E.91, Y.92, V.93, E.94, K.95, N.96, E.99, E.140, N.141, L.143, C.153, D.154 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.20, B:Y.25 Hydrogen bonds: B:V.93, B:V.93

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

SO4.2: 5 residues within 4Å: Chain A: S.145, H.146, N.147, V.149, K.151 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.145, A:N.147 Salt bridges: A:H.146, A:K.151 SO4.3: 4 residues within 4Å: Chain A: F.45, K.46 Chain B: R.176, S.216 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.176, A:K.46 SO4.7: 5 residues within 4Å: Chain B: S.145, H.146, N.147, V.149, K.151 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.145, B:N.147 Salt bridges: B:H.146, B:K.151 SO4.8: 4 residues within 4Å: Chain A: R.176, S.216 Chain B: F.45, K.46 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.46, A:R.176

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: H.125, K.129, E.290 No protein-ligand interaction detected (PLIP) GOL.9: 3 residues within 4Å: Chain B: H.125, K.129, E.290 No protein-ligand interaction detected (PLIP)

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

PEG.5: 4 residues within 4Å: Chain A: D.273, N.277, K.280, Y.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.277, A:K.280 PEG.10: 4 residues within 4Å: Chain B: D.273, N.277, K.280, Y.287 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.277, B:K.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Capener, J.L. et al., Crystal structure of the human CDKL5 kinase domain with compound CAF-382. To Be Published

Release Date

2025-04-02

Peptides

Cyclin-dependent kinase-like 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cyclin-dependent kinase-like 5

Related Entries With Identical Sequence