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KLIFS: A knowledge-based structural database to navigate kinase-ligand interaction space

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Van Linden, Oscar P.J.^, Kooistra, Albert J.^, Leurs, Rob, de Esch, Iwan J.P., de Graaf, Chris

^ = both authors contributed equally to this work

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Directory structure:

<Kinase group>

+--------------<Kinase>

               +---------<PDBcode_alt_chain>

Within each <Kinase group> directory all Kinases with available crystal structures are

listed (<Kinase>). Within the <Kinase> directory all original PDB files are listed

and each subdirectory represents each chain (and if available alternate model) from each available

crystal structure from the PDB for that specific kinase.

EXAMPLE:

CMGC/p38a/1OVE_altA_chainA/

Kinase group is CMGC

Kinase is p38a

The extracted structure is chain A from alternate model A of the crystal structure 1OVE (PDB-code)

Directory contents:

 - <PDBcode_alt_chain>.pdb      # Original PDB chain/model

 - complex.mol2                 # The full superposed complex

 - protein.mol2                 # Protein only

 - pocket.mol2                  # Orthosteric binding pocket as described in the manuscript

 - pocket_residues.aln          # Alignment of the pocket as described in the manuscript

 - atp.mol2*                    # Co-crystallized ATP(-like) molecules

 - staurosporin.mol2*           # Co-crystallized Staurosporin(-like) molecules

 - ions.mol2*                   # Co-crystallized ions

 - organometallics.mol2*        # Co-crystallized organometallics

 - cofactors.mol2*              # Co-crystallized cofactors

 - water.mol2*                  # Observed waters

 - unnatural_aminoacids.mol2*   # unnatural/alternative aminoacids

 - allosteric_ligand.mol2*      # Allosteric ligand(s)

 - ligand.mol2*                 # Orthosteric ligand

 - ifp_aligned.txt*             # The aligned interaction fingerprint

 - fullIFP.txt*                 # Original IFP without any corrections (for gaps/alignment)

 - pocket_RMSD.txt              # RMSD of the two pocket alignments

 - remark*                      # possible problems with the structure are indicated

* Not always present

KLIFS_v1.0.xlsx contains all structural annotations of the orthosteric ligand-bound kinase structures.

                One chain/model per kinase structure was selected for this analysis.