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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
2dc1NADProbable L-aspartate dehydrogenase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2dc1NADProbable L-aspartate dehydrogenase/1.000
2a92NAIL-lactate dehydrogenase/0.524
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.512
5a1tNAIL-lactate dehydrogenase/0.503
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.502
2aa3AP0L-lactate dehydrogenase/0.491
4eb7PLPCysteine desulfurase IscS 2/0.490
1t2cNAIL-lactate dehydrogenase1.1.1.270.489
1yb5NAPQuinone oxidoreductase1.6.5.50.489
1ma0NADAlcohol dehydrogenase class-31.1.1.10.487
3lqfNADGalactitol dehydrogenase/0.487
1x1aSAMC-20 methyltransferase/0.486
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.485
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.485
1tehNADAlcohol dehydrogenase class-31.1.1.10.484
3tjzGNPADP-ribosylation factor 1/0.484
3wswNADL-lactate dehydrogenase/0.484
4i1iNADMalate dehydrogenase/0.483
1mj9COAHistone acetyltransferase ESA1/0.481
1ur5NADMalate dehydrogenase/0.481
2il2LIXRenin3.4.23.150.481
1kp3ATPArgininosuccinate synthase6.3.4.50.480
2a94AP0L-lactate dehydrogenase1.1.1.270.480
3bk2U5PRibonuclease J/0.480
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.480
4eb5PLPCysteine desulfurase IscS 2/0.479
4gl4NAIAlcohol dehydrogenase class-3/0.479
3q43D66M1 family aminopeptidase3.4.110.478
4nd4NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.478
1f8fNADBenzyl alcohol dehydrogenase/0.477
1xe55FEPlasmepsin-23.4.23.390.477
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.477
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.477
1w6hTITPlasmepsin-23.4.23.390.476
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.476
3ai3NDPNADPH-sorbose reductase/0.476
1guyNADMalate dehydrogenase/0.475
3b70NAPEnoyl reductase LovC10.474
3nxxNDPDihydrofolate reductase1.5.1.30.474
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.474
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.473
4yxm2BADNA integrity scanning protein DisA/0.473
4xguADPPutative pachytene checkpoint protein 2/0.472
1uxkNADMalate dehydrogenase/0.471
3d91REMRenin3.4.23.150.471
4m4922YL-lactate dehydrogenase A chain1.1.1.270.471
5jscFADPutative acyl-CoA dehydrogenase/0.471
1xvaSAMGlycine N-methyltransferase2.1.1.200.470
3a3gDLZLumazine protein/0.470
3gvhNADMalate dehydrogenase/0.470
3qlsNDPDihydrofolate reductase1.5.1.30.470
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.470
3dm6757Beta-secretase 13.4.23.460.469
3ig6438Urokinase-type plasminogen activator3.4.21.730.469
2oapANPType II secretion system protein (GspE-2)/0.468
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.468
3vydVYDRenin3.4.23.150.468
4mdhNADMalate dehydrogenase, cytoplasmic1.1.1.370.468
2g1o2IGRenin3.4.23.150.467
2gjlFMNNitronate monooxygenase1.13.12.160.467
1g63FMNEpidermin decarboxylase4.1.10.466
2ifaFMNUncharacterized protein/0.466
3lpkZ76Beta-secretase 13.4.23.460.466
3nsh957Beta-secretase 13.4.23.460.466
3ohh3HHBeta-secretase 13.4.23.460.466
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.466
4i0i957Beta-secretase 13.4.23.460.466
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.465
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.465
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.465
4dd8BATDisintegrin and metalloproteinase domain-containing protein 83.4.240.465
2ex1C5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.464
2gv8NDPThiol-specific monooxygenase1.14.130.464
2p83MR0Beta-secretase 13.4.23.460.464
2x0iNAIMalate dehydrogenase/0.464
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.464
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.463
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.463
2ikuLIYRenin3.4.23.150.463
3lu1NADUDP-N-acetylglucosamine 4-epimerase/0.463
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.462
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.462
3imgBZ2Pantothenate synthetase6.3.2.10.462
4rvgTYDD-mycarose 3-C-methyltransferase/0.462
2g226IGRenin3.4.23.150.461
2iko7IGRenin3.4.23.150.461
3axkNDPRibulose bisphosphate carboxylase large chain4.1.1.390.461
3h3fNAIL-lactate dehydrogenase A chain1.1.1.270.461
3iaaTYDCalG2/0.461
4iv6FDAIsovaleryl-CoA dehydrogenase/0.461
1lbcCYZGlutamate receptor 2/0.460
1udaUFGUDP-glucose 4-epimerase5.1.3.20.460
3b6zCO7Enoyl reductase LovC10.460
3gqvNAPEnoyl reductase LovC10.460
3gw9VNILanosterol 14-alpha-demethylase/0.460
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.460
1mjbACOHistone acetyltransferase ESA1/0.459
1rj6AZMCarbonic anhydrase 144.2.1.10.459
2djxFMNDihydroorotate dehydrogenase (fumarate)1.3.98.10.459
3em3478Gag-Pol polyprotein3.4.23.160.459
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.459
4i9n1E5L-lactate dehydrogenase A chain1.1.1.270.459
1e3eNAIAlcohol dehydrogenase 41.1.1.10.458
1g1aNADdTDP-glucose 4,6-dehydratase/0.458
1icpFMN12-oxophytodienoate reductase 11.3.1.420.458
1me6IVSPlasmepsin-23.4.23.390.458
1v0jFADUDP-galactopyranose mutase5.4.99.90.458
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.458
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.458
4blrUTPNTPase P4/0.458
4yvz3ATDNA integrity scanning protein DisA/0.458
5fl3ADPPili retraction protein PilT/0.458
1b2lNDCAlcohol dehydrogenase1.1.1.10.457
1bim0QBRenin3.4.23.150.457
1fy7COAHistone acetyltransferase ESA1/0.457
1udbUFGUDP-glucose 4-epimerase5.1.3.20.457
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.457
2g1r3IGRenin3.4.23.150.457
3hl0NADMaleylacetate reductase/0.457
3qdlFMNOxygen-insensitive NADPH nitroreductase/0.457
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.457
4opgFDAConserved Archaeal protein/0.457
4twrNADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase/0.457
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.456
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.456
3w8eNAD3-hydroxybutyrate dehydrogenase/0.456
4udrFAD5-(hydroxymethyl)furfural oxidase/0.456
5e5h0T1Succinyl-CoA:acetate CoA-transferase/0.456
1emdNADMalate dehydrogenase/0.455
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.455
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.455
2w3bNDPDihydrofolate reductase1.5.1.30.455
3ge6FMNNitroreductase/0.455
3ieuGDPGTPase Era/0.455
4dfg0JVGag-Pol polyprotein3.4.23.160.455
4m83ERYOleandomycin glycosyltransferase2.4.10.455
1qyvNAPEstradiol 17-beta-dehydrogenase 11.1.1.620.454
1y7lASN_LEU_ASN_ILECysteine synthase2.5.1.470.454
2g1y5IGRenin3.4.23.150.454
2omeNADC-terminal-binding protein 2/0.454
2ylrNAPPhenylacetone monooxygenase1.14.13.920.454
3k5c0BIBeta-secretase 13.4.23.460.454
3tr05GPGuanylate kinase/0.454
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.454
4mihFADPyranose 2-oxidase1.1.3.100.454
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.453
3etdNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.453
3lpjZ75Beta-secretase 13.4.23.460.453
3u33FADPutative acyl-CoA dehydrogenase AidB1.3.990.453
4g7gVFVLanosterol 14-alpha-demethylase/0.453
4rvfTYDD-mycarose 3-C-methyltransferase/0.453
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.453
1hyhNADL-2-hydroxyisocaproate dehydrogenase/0.452
1lwiNAP3-alpha-hydroxysteroid dehydrogenase1.1.1.500.452
1xe65FPPlasmepsin-23.4.23.390.452
2c20NADUDP-glucose 4-epimerase/0.452
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.452
2iibC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.452
3cib314Beta-secretase 13.4.23.460.452
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.452
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.452
1szgFNSCytochrome b2, mitochondrial1.1.2.30.451
2vwqNAPGlucose 1-dehydrogenase/0.451
2xhd7T9Glutamate receptor 2/0.451
2xx91NFGlutamate receptor 2/0.451
2ztmNADD(-)-3-hydroxybutyrate dehydrogenase/0.451
3dg8NDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.451
4a8v2ANMajor pollen allergen Bet v 1-J/0.451
4ejmNAPPutative zinc-binding dehydrogenase/0.451
4eu8COASuccinyl-CoA:acetate CoA-transferase/0.451
5czySAMEukaryotic huntingtin interacting protein B/0.451
1mjaCOAHistone acetyltransferase ESA1/0.450
1xl5190Gag-Pol polyprotein3.4.23.160.450
2ag5NAD3-hydroxybutyrate dehydrogenase type 2/0.450
2g1s4IGRenin3.4.23.150.450
3ai2NDPNADPH-sorbose reductase/0.450
3duyAFJBeta-secretase 13.4.23.460.450
3qe2FMNNADPH--cytochrome P450 reductase/0.450
3s1dZIRCytokinin dehydrogenase 11.5.99.120.450
4ewo996Beta-secretase 13.4.23.460.450
4h8aNAIUreidoglycolate dehydrogenase (NAD(+))1.1.1.3500.450
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.449
2dftADPShikimate kinase2.7.1.710.449
2wf1ZY1Beta-secretase 13.4.23.460.449
3h3jNADL-lactate dehydrogenase 11.1.1.270.449
3o0o5ADVitamin B12-dependent ribonucleotide reductase/0.449
3qbhQBHBeta-secretase 13.4.23.460.449
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.449
4fse0VABeta-secretase 13.4.23.460.449
4oztP1AEcdysone receptor, putative/0.449
1aa6MGDFormate dehydrogenase H1.1.99.330.448
1icsFMN12-oxophytodienoate reductase 11.3.1.420.448
1obbNADAlpha-glucosidase3.2.1.200.448
2bi8FADUDP-galactopyranose mutase5.4.99.90.448
2givACOHistone acetyltransferase KAT8/0.448
2i7pACOPantothenate kinase 32.7.1.330.448
3atrFDAConserved Archaeal protein/0.448
3fhyATPPyridoxal kinase2.7.1.350.448
4b79NADProbable short-chain dehydrogenase/0.448
4lnbED5CaaX farnesyltransferase beta subunit Ram1/0.448
1gpdNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.447
1psa0ZLPepsin A3.4.23.10.447
1tqf32PBeta-secretase 13.4.23.460.447
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.447
2i4qUA4Renin3.4.23.150.447
2q1tNADPutative nucleotide sugar epimerase/ dehydratase/0.447
2ywlFADThioredoxin reductase related protein/0.447
3cic316Beta-secretase 13.4.23.460.447
3lpiZ74Beta-secretase 13.4.23.460.447
3mk6ACOPantothenate kinase 32.7.1.330.447
3r7kFDAProbable acyl CoA dehydrogenase/0.447
3wqmB29Diterpene synthase3.1.7.80.447
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.447
4i9h1E4L-lactate dehydrogenase A chain1.1.1.270.447
4lxa1YSBeta-secretase 13.4.23.460.447
1q6t600Tyrosine-protein phosphatase non-receptor type 13.1.3.480.446
1xddAAYIntegrin alpha-L/0.446
2ejvNADL-threonine 3-dehydrogenase/0.446
2g247IGRenin3.4.23.150.446
2zvbSAHPrecorrin-3 C17-methyltransferase/0.446
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.446
3veu0GOBeta-secretase 13.4.23.460.446
3vf30GSBeta-secretase 13.4.23.460.446
5a3bAPRSIR2 family protein/0.446
1gheACOAcetyltransferase2.3.10.445
1n7hNDPGDP-mannose 4,6 dehydratase 24.2.1.470.445
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.445
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.445
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.445
2igoFADPyranose 2-oxidase/0.445
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.445
3djjFADGlutathione reductase, mitochondrial1.8.1.70.445
3to6LYS_CMCHistone acetyltransferase ESA1/0.445
4gavFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.445
4lutDCSAlanine racemase/0.445
4q71FADBifunctional protein PutA/0.445
4x28FDAAcyl-CoA dehydrogenase FadE26/0.445
4x28FDAAcyl-CoA dehydrogenase FadE27/0.445
4yaw2AMNADPH--cytochrome P450 reductase/0.445
1bil0IURenin3.4.23.150.444
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.444
1rneC60Renin3.4.23.150.444
2ien017Gag-Pol polyprotein3.4.23.160.444
2vyqFADFerredoxin--NADP reductase1.18.1.20.444
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.444
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
1geeNADGlucose 1-dehydrogenase1.1.1.470.443
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.443
1pzfA3DLactate dehydrogenase/0.443
1qorNDPQuinone oxidoreductase 1/0.443
1rfuADPPyridoxal kinase2.7.1.350.443
2b4rAESGlyceraldehyde-3-phosphate dehydrogenase/0.443
2hu2NADC-terminal binding protein 1/0.443
2i3gNAPN-acetyl-gamma-glutamyl-phosphate reductase1.2.1.380.443
2ilvC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.443
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.443
3ahn3A1Oligopeptidase/0.443
3qt62P0Mevalonate diphosphate decarboxylase/0.443
3uylTYDProbable NDP-rhamnosyltransferase/0.443
4euaCOASuccinyl-CoA:acetate CoA-transferase/0.443
4g6gFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.443
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.443
4h1vGNPDynamin-1-like protein3.6.5.50.443
5c77SAHProtein arginine N-methyltransferase SFM1/0.443
1amoFMNNADPH--cytochrome P450 reductase/0.442
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1x27ASP_TYR_VAL_HIS_PTRTyrosine-protein kinase Lck2.7.10.20.442
1xkdNAPIsocitrate dehydrogenase [NADP]/0.442
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.442
2hizLIJBeta-secretase 13.4.23.460.442
2yxuATPPyridoxal kinase2.7.1.350.442
2zvcSAHPrecorrin-3 C17-methyltransferase/0.442
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.442
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.442
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.442
3hyoADPPyridoxal kinase/0.442
3mvqNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.442
3rpeFADPutative modulator of drug activity/0.442
3ruaNADUDP-N-acetylglucosamine 4-epimerase/0.442
3toxNAPPutative oxidoreductase/0.442
3u9eCOALmo1369 protein/0.442
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.442
4j75TYMTryptophan--tRNA ligase/0.442
4m9aFDAAcyl-CoA dehydrogenase/0.442
4p53NAI2-epi-5-epi-valiolone synthase/0.442
5kwvANPPantothenate synthetase/0.442
1pzgA3DLactate dehydrogenase/0.441
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.441
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.441
1uxjNADMalate dehydrogenase/0.441
1yqdNAPSinapyl alcohol dehydrogenase/0.441
2hldANPATP synthase subunit alpha, mitochondrial/0.441
2hldANPATP synthase subunit beta, mitochondrial3.6.3.140.441
2hpvFMNFMN-dependent NADH-azoreductase1.70.441
2iqgF2IBeta-secretase 13.4.23.460.441
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.441
3lqsPSZD-alanine aminotransferase2.6.1.210.441
3m6iNADL-arabinitol 4-dehydrogenase1.1.1.120.441
3sglFADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC/0.441
4ajn88VL-lactate dehydrogenase A chain1.1.1.270.441
4lcjNADC-terminal-binding protein 2/0.441
4uunNAIL-lactate dehydrogenase/0.441
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.440
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.440
1udyFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.440
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
2jcxNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.440
3c212BADNA integrity scanning protein DisA/0.440
3cid318Beta-secretase 13.4.23.460.440
3k5gBJCBeta-secretase 13.4.23.460.440
3kb1ADPIron-sulfur cluster carrier protein/0.440
3kgcLY7Glutamate receptor 2/0.440
3v2uATPProtein GAL3/0.440
3vx4ATPPutative ABC transporter, ATP-binding protein ComA/0.440
4ambDUDPutative glycosyl transferase/0.440
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.440
4gsuDWZL,D-transpeptidase 22.3.20.440
4nbwNADShort-chain dehydrogenase/reductase SDR/0.440