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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
3wycNAPMeso-diaminopimelate D-dehydrogenase1.4.1.16

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3wycNAPMeso-diaminopimelate D-dehydrogenase1.4.1.161.000
3wbbNAPMeso-diaminopimelate D-dehydrogenase/0.502
1f06NDPMeso-diaminopimelate D-dehydrogenase1.4.1.160.496
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.479
2a92NAIL-lactate dehydrogenase/0.477
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.471
1bwsNDPGDP-L-fucose synthase/0.470
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.470
4q71FADBifunctional protein PutA/0.465
1x1aSAMC-20 methyltransferase/0.463
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.459
4rvgTYDD-mycarose 3-C-methyltransferase/0.459
4yaoFMNNADPH--cytochrome P450 reductase/0.459
4dbzNDPPutative ketoacyl reductase1.3.10.458
1xe55FEPlasmepsin-23.4.23.390.457
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.457
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.457
1qrpHH0Pepsin A-43.4.23.10.456
3gvhNADMalate dehydrogenase/0.455
1g6kNADGlucose 1-dehydrogenase1.1.1.470.454
1icpFMN12-oxophytodienoate reductase 11.3.1.420.452
4djaFAD(6-4) photolyase/0.452
4rvfTYDD-mycarose 3-C-methyltransferase/0.452
1tehNADAlcohol dehydrogenase class-31.1.1.10.451
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.451
4i1iNADMalate dehydrogenase/0.451
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.451
4lcjNADC-terminal-binding protein 2/0.451
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
1h51FMNPentaerythritol tetranitrate reductase/0.450
3hwrNDP2-dehydropantoate 2-reductase/0.450
4eb7PLPCysteine desulfurase IscS 2/0.450
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.450
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
4dc0NDPPutative ketoacyl reductase1.3.10.449
4g74FADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.449
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.448
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.448
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.447
2cy0NAPShikimate dehydrogenase (NADP(+))/0.447
3qt62P0Mevalonate diphosphate decarboxylase/0.447
4ypuSAMHistone-lysine N-methyltransferase ASH1L2.1.1.430.447
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
2gv8NDPThiol-specific monooxygenase1.14.130.446
3c1y2BADNA integrity scanning protein DisA/0.446
4g9kFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.446
5irnADPNucleotide binding oligomerization domain containing 2/0.446
2ejvNADL-threonine 3-dehydrogenase/0.445
2yoj8Y6Genome polyprotein2.7.7.480.445
3gfbNADL-threonine 3-dehydrogenase/0.445
3p62FMNPentaerythritol tetranitrate reductase/0.445
4mdhNADMalate dehydrogenase, cytoplasmic1.1.1.370.444
5kwvANPPantothenate synthetase/0.444
2i7pACOPantothenate kinase 32.7.1.330.443
2g226IGRenin3.4.23.150.442
3tjzGNPADP-ribosylation factor 1/0.442
3x2eNAIAdenosylhomocysteinase/0.442
4ure1PSCyclohexanol dehydrogenase/0.442
1h63FMNPentaerythritol tetranitrate reductase/0.441
3fp0FP015-O-acetyltransferase/0.441
3hl0NADMaleylacetate reductase/0.441
1n2sNAIdTDP-4-dehydrorhamnose reductase1.1.1.1330.440
2dfvNADL-threonine 3-dehydrogenase/0.440
3drcMTXDihydrofolate reductase1.5.1.30.440
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.440