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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
1bmdNADMalate dehydrogenase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1bmdNADMalate dehydrogenase/1.000
1wzeNADMalate dehydrogenase/0.687
1bdmNAXMalate dehydrogenase/0.639
1wziNDPMalate dehydrogenase/0.621
2cvqNDPMalate dehydrogenase/0.592
1b8vNADMalate dehydrogenase/0.572
1b8uNADMalate dehydrogenase/0.560
1y7tNDPMalate dehydrogenase/0.552
2a92NAIL-lactate dehydrogenase/0.522
4uunNAIL-lactate dehydrogenase/0.517
4i1iNADMalate dehydrogenase/0.514
1llqNADNAD-dependent malic enzyme, mitochondrial1.1.1.380.506
3h3fNAIL-lactate dehydrogenase A chain1.1.1.270.502
1t2cNAIL-lactate dehydrogenase1.1.1.270.500
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.499
4rlsNAIL-lactate dehydrogenase A chain1.1.1.270.499
1o0sNAINAD-dependent malic enzyme, mitochondrial1.1.1.380.496
4i8x6P3L-lactate dehydrogenase A chain1.1.1.270.495
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.484
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.475
2x0rNADMalate dehydrogenase/0.474
3ijoB4DGlutamate receptor 2/0.472
4mdhNADMalate dehydrogenase, cytoplasmic1.1.1.370.472
1ur5NADMalate dehydrogenase/0.471
3gvhNADMalate dehydrogenase/0.468
1p0hACOMycothiol acetyltransferase2.3.1.1890.467
1xe65FPPlasmepsin-23.4.23.390.466
2a94AP0L-lactate dehydrogenase1.1.1.270.465
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.465
2ebaFADPutative glutaryl-CoA dehydrogenase/0.465
3wswNADL-lactate dehydrogenase/0.465
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.465
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.464
1jpaANPEphrin type-B receptor 22.7.10.10.462
2po7CHDFerrochelatase, mitochondrial4.99.1.10.462
4irnFADAnaB/0.462
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
1kvkATPMevalonate kinase2.7.1.360.460
2xyuQ9GEphrin type-A receptor 42.7.10.10.460
3m6iNADL-arabinitol 4-dehydrogenase1.1.1.120.459
1mjaCOAHistone acetyltransferase ESA1/0.458
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.458
2ldbNADL-lactate dehydrogenase1.1.1.270.458
4i9h1E4L-lactate dehydrogenase A chain1.1.1.270.458
1uxkNADMalate dehydrogenase/0.457
3to6LYS_CMCHistone acetyltransferase ESA1/0.457
4iv6FDAIsovaleryl-CoA dehydrogenase/0.457
2y0mACOHistone acetyltransferase KAT8/0.456
3lqfNADGalactitol dehydrogenase/0.456
4enhFVXCholesterol 24-hydroxylase/0.456
4ktl1CQCytochrome P450/0.456
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.456
1ez4NADL-lactate dehydrogenase1.1.1.270.455
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.455
1lbcCYZGlutamate receptor 2/0.455
1tqf32PBeta-secretase 13.4.23.460.455
3a1nNADNDP-sugar epimerase/0.455
4dbzNDPPutative ketoacyl reductase1.3.10.455
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.454
2ou2ACOHistone acetyltransferase KAT5/0.454
3ik6HCZGlutamate receptor 2/0.454
4ejmNAPPutative zinc-binding dehydrogenase/0.454
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.454
4r81FMNPredicted NADH dehydrogenase/0.454
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
3gobHXXDdmC/0.451
3oetNADErythronate-4-phosphate dehydrogenase/0.451
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.451
4nmdFDABifunctional protein PutA/0.451
1guyNADMalate dehydrogenase/0.450
2x0iNAIMalate dehydrogenase/0.450
3gy0NAPNAD(P)-dependent oxidoreductase/0.450
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.450
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.450
2cwfNDPDelta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase/0.449
3hl0NADMaleylacetate reductase/0.449
2c27ACOMycothiol acetyltransferase2.3.1.1890.448
2jcxNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.448
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.448
4rvfTYDD-mycarose 3-C-methyltransferase/0.447
1mjbACOHistone acetyltransferase ESA1/0.446
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.446
2g8yNADHydroxycarboxylate dehydrogenase B/0.446
2hldANPATP synthase subunit alpha, mitochondrial/0.446
2hldANPATP synthase subunit beta, mitochondrial3.6.3.140.446
3ieuGDPGTPase Era/0.446
3kb1ADPIron-sulfur cluster carrier protein/0.446
1qrpHH0Pepsin A-43.4.23.10.445
1t9gFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.445
3fhyATPPyridoxal kinase2.7.1.350.445
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.445
4an4DUDPutative glycosyl transferase/0.445
4mk728OGenome polyprotein2.7.7.480.445
4u9yCOAAlpha-tubulin N-acetyltransferase 1/0.445
2g1n1IGRenin3.4.23.150.444
2ifaFMNUncharacterized protein/0.444
2vwqNAPGlucose 1-dehydrogenase/0.444
3hyoADPPyridoxal kinase/0.444
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.444
4i9n1E5L-lactate dehydrogenase A chain1.1.1.270.444
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.444
4xj3GTPCyclic GMP-AMP synthase/0.444
1udaUFGUDP-glucose 4-epimerase5.1.3.20.443
1yb5NAPQuinone oxidoreductase1.6.5.50.443
3d4pNADL-lactate dehydrogenase 11.1.1.270.443
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.443
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.443
4e2dFMNDehydrogenase/0.443
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.443
1fy7COAHistone acetyltransferase ESA1/0.442
1k6pXN3Gag-Pol polyprotein3.4.23.160.442
1pjcNADAlanine dehydrogenase/0.442
2b7aIZATyrosine-protein kinase JAK2/0.442
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.442
2p2xSAHDiphthine synthase/0.442
3a4vNADNDP-sugar epimerase/0.442
4ambDUDPutative glycosyl transferase/0.442
4m83ERYOleandomycin glycosyltransferase2.4.10.442
1a72PADAlcohol dehydrogenase E chain1.1.1.10.441
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1hncGDNGlutathione S-transferase Mu 22.5.1.180.441
2ejzSAHDiphthine synthase/0.441
2y3rTRKTamL/0.441
3lu1NADUDP-N-acetylglucosamine 4-epimerase/0.441
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.441
4j7uNAPSepiapterin reductase1.1.1.1530.441
1ib6NADMalate dehydrogenase/0.440
1ipeNDPTropinone reductase 21.1.1.2360.440
1iyzNDPProbable quinone oxidoreductase/0.440
2bu9HFVIsopenicillin N synthase1.21.3.10.440
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.440
2nruT12Interleukin-1 receptor-associated kinase 42.7.11.10.440
2w6zL21Biotin carboxylase6.3.4.140.440
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4kwhNAPReductase homolog/0.440
5d3qGDPDynamin-13.6.5.50.440