SMTL ID : 5n3j.1

cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule 4-Nitrobenzoic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

monomer

Ligands

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 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.103, A:Y.309 Hydrogen bonds: A:E.158 Water bridges: A:K.295

1 x 4NB: 4-NITROBENZOIC ACID(Non-covalent)

4NB.2: 13 residues within 4Å: Chain A: L.52, V.60, A.73, K.75, V.107, M.123, E.124, Y.125, V.126, L.176, T.186, D.187, F.330 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.60, A:A.73, A:M.123, A:T.186 Hydrogen bonds: A:D.187 Water bridges: A:K.75, A:K.75, A:K.75, A:F.188 Salt bridges: A:K.75

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

DMS.3: 5 residues within 4Å: Chain A: F.21, K.24, A.25, E.28, N.102 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.102 Salt bridges: A:E.28 DMS.4: 5 residues within 4Å: Chain A: W.33, L.92, N.93, R.96, E.352 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.96 Salt bridges: A:E.352

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. (2020)

Release Date

2018-02-28

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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