SMTL ID : 6t29.1

Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 18 (CS587)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: E.17, S.90, P.91, N.92, H.93 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.90, A:N.92, A:N.92, A:H.93 Water bridges: A:S.90, A:Y.95, A:Y.95, A:Y.95 Salt bridges: A:H.93 SO4.7: 8 residues within 4Å: Chain A: Y.133, H.136, R.137, K.200, C.204, T.269, C.270, E.271 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.270, A:E.271 Water bridges: A:E.271 Salt bridges: A:H.136, A:R.137, A:K.200 SO4.8: 3 residues within 4Å: Chain A: Y.244, Q.296, K.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.244, A:Q.296 Salt bridges: A:K.299 SO4.9: 6 residues within 4Å: Chain A: L.59, K.60, G.61, K.62, E.63, S.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.61, A:E.63, A:S.64

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

EDO.2: 7 residues within 4Å: Chain A: L.73, I.76, V.82, A.83, L.84, Y.134, F.166 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.82, A:L.84, A:Y.134, A:Y.134 Water bridges: A:I.76 EDO.3: 3 residues within 4Å: Chain A: D.130, Y.133, A.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.130, A:D.130 EDO.4: 6 residues within 4Å: Chain A: V.101, S.102, G.103, G.104, E.105 Ligands: M8Z.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.101, A:G.104, A:E.105 EDO.5: 3 residues within 4Å: Chain A: P.219, Y.222, N.300 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.300 EDO.6: 6 residues within 4Å: Chain A: K.52, L.96, M.98, F.166, G.167, L.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.168

1 x M8Z: 2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[3,5-bis(2-cyanopropan-2-yl)phenyl]amino]pyrimidine-5-carboxamide(Non-covalent)

M8Z.10: 16 residues within 4Å: Chain A: E.27, L.29, V.37, A.50, V.82, Q.99, L.100, V.101, S.102, E.105, E.148, N.149, L.151, S.164, D.165 Ligands: EDO.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.29, A:L.151 Hydrogen bonds: A:Q.99, A:V.101, A:V.101, A:N.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fromont, C. et al., Discovery of Highly Selective Inhibitors of Calmodulin-Dependent Kinases That Restore Insulin Sensitivity in the Diet-Induced Obesityin VivoMouse Model. J.Med.Chem. (2020)

Release Date

2019-11-13

Peptides

Calcium/calmodulin-dependent protein kinase type 1D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Calcium/calmodulin-dependent protein kinase type 1D

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