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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
3pymNADGlyceraldehyde-3-phosphate dehydrogenase 31.2.1.12

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3pymNADGlyceraldehyde-3-phosphate dehydrogenase 31.2.1.121.000
4p8rNADGlyceraldehyde-3-phosphate dehydrogenase/0.665
3idsNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.654
1gadNADGlyceraldehyde-3-phosphate dehydrogenase A/0.652
1rm5NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.598
3dmtNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.593
3v1yNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.588
1dc6NADGlyceraldehyde-3-phosphate dehydrogenase A/0.583
1j0xNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.582
1u8fNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.578
1znqNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.574
3cpsNADGlyceraldehyde-3-phosphate dehydrogenase/0.572
2b4rNADGlyceraldehyde-3-phosphate dehydrogenase/0.569
4z0hNADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic1.2.1.120.566
1dbvNADGlyceraldehyde-3-phosphate dehydrogenase/0.561
1vsvNADGlyceraldehyde-3-phosphate dehydrogenase/0.557
3ksdNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.556
1ihyAPRGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.549
3l0dNADGlyceraldehyde-3-phosphate dehydrogenase/0.549
3cmcNADGlyceraldehyde-3-phosphate dehydrogenase/0.544
4boyNADGlyceraldehyde-3-phosphate dehydrogenase/0.544
4lsmNADGlyceraldehyde-3-phosphate dehydrogenase/0.543
5c7oNADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific1.2.1.120.543
1vc2NADGlyceraldehyde-3-phosphate dehydrogenase/0.541
1gaeNADGlyceraldehyde-3-phosphate dehydrogenase A/0.536
1ywgNADGlyceraldehyde-3-phosphate dehydrogenase/0.529
2ep7NADGlyceraldehyde-3-phosphate dehydrogenase/0.528
4dbvNDPGlyceraldehyde-3-phosphate dehydrogenase/0.526
1jn0NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.522
1ihxSNDGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.521
1szjNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.520
3zcxNADGlyceraldehyde-3-phosphate dehydrogenase/0.519
3gnqNADGlyceraldehyde-3-phosphate dehydrogenase/0.518
1rm3NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.516
3hjaNADGlyceraldehyde-3-phosphate dehydrogenase/0.513
2dbvNDPGlyceraldehyde-3-phosphate dehydrogenase/0.510
4o63NADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.501
1nqaNADGlyceraldehyde-3-phosphate dehydrogenase/0.498
3k2bNADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.496
1nboNADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.494
3l4sNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.486
3zhbNAPPutative dehydrogenase/0.468
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.450
2gjlFMNNitronate monooxygenase1.13.12.160.450
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
2o23NAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.447
4q71FADBifunctional protein PutA/0.447
2he5NDPAldo-keto reductase family 1 member C211.1.10.446
1w6hTITPlasmepsin-23.4.23.390.445
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.444
4dbzNDPPutative ketoacyl reductase1.3.10.443
4l4xNDPAmphI/0.442
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.442
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
3hl0NADMaleylacetate reductase/0.441
3b70NAPEnoyl reductase LovC10.440
4q73FADBifunctional protein PutA/0.440