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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3pd5TSBThreonine--tRNA ligase6.1.1.3

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3pd5TSBThreonine--tRNA ligase6.1.1.31.000
2hl2SSAThreonine--tRNA ligase6.1.1.30.631
2hl1A3SThreonine--tRNA ligase6.1.1.30.614
3pd2A3SThreonine--tRNA ligase6.1.1.30.563
4rrqA3SThreonine--tRNA ligase6.1.1.30.562
3pd4A3GThreonine--tRNA ligase6.1.1.30.557
4rrgA3TThreonine--tRNA ligase6.1.1.30.547
4rrfA3SThreonine--tRNA ligase6.1.1.30.539
4rrrA3TThreonine--tRNA ligase6.1.1.30.528
3pd3A3TThreonine--tRNA ligase6.1.1.30.524
4rrhA3SProbable threonine--tRNA ligase 26.1.1.30.512
4rraA3TProbable threonine--tRNA ligase 26.1.1.30.498
4rriA3TProbable threonine--tRNA ligase 26.1.1.30.487
4rr8A3SProbable threonine--tRNA ligase 26.1.1.30.483
2hl0A3SThreonine--tRNA ligase6.1.1.30.477
4rr7A3SProbable threonine--tRNA ligase 26.1.1.30.473
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.471
4rrbA3TProbable threonine--tRNA ligase 26.1.1.30.469
4rr6A3SProbable threonine--tRNA ligase 26.1.1.30.467
5iubCLRAdenosine receptor A2a/0.467
4rr9A3SProbable threonine--tRNA ligase 26.1.1.30.465
5iu86DZAdenosine receptor A2a/0.460
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.459
5k2cZMAAdenosine receptor A2a/0.459
4rrmA3TProbable threonine--tRNA ligase 26.1.1.30.456
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.455
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
4rrlA3SProbable threonine--tRNA ligase 26.1.1.30.451
5h8tRTLRetinol-binding protein 1/0.450
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
3sn6P0GBeta-2 adrenergic receptor/0.448
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3q5kD1UHeat shock protein 83-1/0.447
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.446
4rrjA3SProbable threonine--tRNA ligase 26.1.1.30.446
4s0vSUVOrexin receptor type 2/0.446
4rrdA3TProbable threonine--tRNA ligase 26.1.1.30.444
3dpd41APhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4obuPLPPyridoxal-dependent decarboxylase domain protein/0.443
1fxsNAPGDP-L-fucose synthase/0.441
4rrkA3TProbable threonine--tRNA ligase 26.1.1.30.441
1r2jFADFkbI/0.440
2rhrEMOPutative ketoacyl reductase1.3.10.440
3q43D66M1 family aminopeptidase3.4.110.440
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4fa60TAPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440