SMTL ID : 6z44.1

Crystal structure of the cAMP-dependent protein kinase A in complex with phenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

monomer

Ligands

1 x IPH: PHENOL(Non-covalent)

IPH.1: 10 residues within 4Å: Chain A: L.52, V.60, A.73, M.123, E.124, Y.125, V.126, L.176, T.186, F.330 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.60, A:L.176, A:L.176, A:F.330 Hydrogen bonds: A:V.126

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 5 residues within 4Å: Chain A: N.39, T.40, A.41, Q.42, H.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.39 DMS.3: 6 residues within 4Å: Chain A: L.201, C.202, G.203, P.205, L.208, Y.250 No protein-ligand interaction detected (PLIP) DMS.4: 4 residues within 4Å: Chain A: F.21, K.24, A.25, Y.309 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.28

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.5: 10 residues within 4Å: Chain A: V.18, F.21, L.22, F.103, L.155, E.158, Y.159, K.295, I.306, Y.309 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.18, A:F.21, A:F.21, A:Y.309 Hydrogen bonds: A:L.155 Water bridges: A:K.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oebbeke, M. et al., Fragment Binding to Kinase Hinge: If Charge Distribution and Local pK a Shifts Mislead Popular Bioisosterism Concepts. Angew.Chem.Int.Ed.Engl. (2021)

Release Date

2020-12-09

Peptides

cAMP-dependent protein kinase catalytic subunit alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

cAMP-dependent protein kinase catalytic subunit alpha

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