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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
1dbvNADGlyceraldehyde-3-phosphate dehydrogenase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1dbvNADGlyceraldehyde-3-phosphate dehydrogenase/1.000
1gd1NADGlyceraldehyde-3-phosphate dehydrogenase/0.639
2dbvNDPGlyceraldehyde-3-phosphate dehydrogenase/0.637
1u8fNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.617
1rm4NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.611
3cmcNADGlyceraldehyde-3-phosphate dehydrogenase/0.606
3hjaNADGlyceraldehyde-3-phosphate dehydrogenase/0.601
4dbvNDPGlyceraldehyde-3-phosphate dehydrogenase/0.600
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.598
3lvfNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.597
3ksdNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.594
3cifNADGlyceraldehyde-3-phosphate dehydrogenase/0.593
4lsmNADGlyceraldehyde-3-phosphate dehydrogenase/0.592
1ml3NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.591
2ep7NADGlyceraldehyde-3-phosphate dehydrogenase/0.590
1rm5NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.589
1nboNADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.588
1vc2NADGlyceraldehyde-3-phosphate dehydrogenase/0.588
1nptNADGlyceraldehyde-3-phosphate dehydrogenase/0.587
4boyNADGlyceraldehyde-3-phosphate dehydrogenase/0.587
1gypNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.586
3e5rNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.585
3k2bNADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.584
1nq5NADGlyceraldehyde-3-phosphate dehydrogenase/0.580
3l4sNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.580
4o59NADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.580
3gnqNADGlyceraldehyde-3-phosphate dehydrogenase/0.579
1rm3NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.576
1dc6NADGlyceraldehyde-3-phosphate dehydrogenase A/0.574
3idsNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.573
4p8rNADGlyceraldehyde-3-phosphate dehydrogenase/0.570
4z0hNADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic1.2.1.120.568
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.567
1qxsNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.566
3zcxNADGlyceraldehyde-3-phosphate dehydrogenase/0.565
3v1yNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.564
5c7oNADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific1.2.1.120.564
2pkrNDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.562
3cpsNADGlyceraldehyde-3-phosphate dehydrogenase/0.558
1nqoNADGlyceraldehyde-3-phosphate dehydrogenase/0.556
1jn0NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.539
1szjNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.536
2b4rNADGlyceraldehyde-3-phosphate dehydrogenase/0.536
2vynNADGlyceraldehyde-3-phosphate dehydrogenase A/0.536
1znqNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.534
1ihxSNDGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.529
1vsvNADGlyceraldehyde-3-phosphate dehydrogenase/0.529
2d2iNAPGlyceraldehyde-3-phosphate dehydrogenase/0.527
3pymNADGlyceraldehyde-3-phosphate dehydrogenase 31.2.1.120.527
3dmtNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.515
2vyvNADGlyceraldehyde-3-phosphate dehydrogenase A/0.508
1ywgNADGlyceraldehyde-3-phosphate dehydrogenase/0.505
1cerNADGlyceraldehyde-3-phosphate dehydrogenase/0.503
4o63NADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.500
1gadNADGlyceraldehyde-3-phosphate dehydrogenase A/0.498
1dssNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.490
2g82NADGlyceraldehyde-3-phosphate dehydrogenase/0.486
3umvFADDeoxyribodipyrimidine photo-lyase4.1.99.30.480
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.477
3l0dNADGlyceraldehyde-3-phosphate dehydrogenase/0.475
1nqaNADGlyceraldehyde-3-phosphate dehydrogenase/0.473
1ihyAPRGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.459
4dreNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.458
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.457
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.455
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.454
1j0xNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.453
3a1nNADNDP-sugar epimerase/0.453
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
1bwsNDPGDP-L-fucose synthase/0.449
1jipKTN6-deoxyerythronolide B hydroxylase/0.449
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
3qv1NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.449
3zc3NAPFerredoxin--NADP reductase1.18.1.20.449
4yaoFMNNADPH--cytochrome P450 reductase/0.449
1jioDEB6-deoxyerythronolide B hydroxylase/0.448
1llqNADNAD-dependent malic enzyme, mitochondrial1.1.1.380.448
2b4qNAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.448
1bk0ACVIsopenicillin N synthase1.21.3.10.447
2iviACWIsopenicillin N synthase1.21.3.10.445
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.445
1jolFFODihydrofolate reductase1.5.1.30.443
1xe55FEPlasmepsin-23.4.23.390.443
2vwqNAPGlucose 1-dehydrogenase/0.443
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.442
2givACOHistone acetyltransferase KAT8/0.442
2ph5NADHomospermidine synthase/0.442
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.442
1nzdUPGDNA beta-glucosyltransferase/0.441
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.441
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.440
2y60M8FIsopenicillin N synthase1.21.3.10.440
3gobHXXDdmC/0.440