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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
1emdNADMalate dehydrogenase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1emdNADMalate dehydrogenase/1.000
1ib6NADMalate dehydrogenase/0.633
4mdhNADMalate dehydrogenase, cytoplasmic1.1.1.370.571
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.566
2aa3AP0L-lactate dehydrogenase/0.556
2a94AP0L-lactate dehydrogenase1.1.1.270.552
3h3jNADL-lactate dehydrogenase 11.1.1.270.550
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.545
4rosAPRMalate dehydrogenase/0.537
3d4pNADL-lactate dehydrogenase 11.1.1.270.534
2hjrAPRMalate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase/0.533
1t2cNAIL-lactate dehydrogenase1.1.1.270.528
4nd4NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.528
1uxjNADMalate dehydrogenase/0.526
1pzgA3DLactate dehydrogenase/0.525
1pzhNADLactate dehydrogenase/0.524
1gv0NADMalate dehydrogenase/0.523
2a92NAIL-lactate dehydrogenase/0.522
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.522
1ur5NADMalate dehydrogenase/0.521
3h3fNAIL-lactate dehydrogenase A chain1.1.1.270.510
1ez4NADL-lactate dehydrogenase1.1.1.270.509
1uxkNADMalate dehydrogenase/0.508
5a1tNAIL-lactate dehydrogenase/0.508
1guyNADMalate dehydrogenase/0.505
1b8vNADMalate dehydrogenase/0.501
4wlvNADMalate dehydrogenase, mitochondrial1.1.1.370.499
4i1iNADMalate dehydrogenase/0.497
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.496
3rpeFADPutative modulator of drug activity/0.496
4l4sNAIL-lactate dehydrogenase A chain1.1.1.270.496
2ldbNADL-lactate dehydrogenase1.1.1.270.495
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.494
2dc1NADProbable L-aspartate dehydrogenase/0.494
4ajn88VL-lactate dehydrogenase A chain1.1.1.270.493
4rlsNAIL-lactate dehydrogenase A chain1.1.1.270.490
1sowNADL-lactate dehydrogenase1.1.1.270.489
3gvhNADMalate dehydrogenase/0.489
3ohh3HHBeta-secretase 13.4.23.460.489
1w4xFADPhenylacetone monooxygenase1.14.13.920.484
3wswNADL-lactate dehydrogenase/0.481
4gl4NAIAlcohol dehydrogenase class-3/0.480
4i9n1E5L-lactate dehydrogenase A chain1.1.1.270.479
4g7gVFVLanosterol 14-alpha-demethylase/0.478
2wsbNADGalactitol dehydrogenase/0.477
4uunNAIL-lactate dehydrogenase/0.475
3b6zCO7Enoyl reductase LovC10.474
4u0mGTPCyclic GMP-AMP synthase/0.474
1tehNADAlcohol dehydrogenase class-31.1.1.10.473
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.472
4i8x6P3L-lactate dehydrogenase A chain1.1.1.270.471
4jjiNADAlcohol dehydrogenase class-3/0.471
4xguADPPutative pachytene checkpoint protein 2/0.471
1nzdUPGDNA beta-glucosyltransferase/0.470
2ylzFADPhenylacetone monooxygenase1.14.13.920.469
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.468
2y05NAPProstaglandin reductase 1/0.468
4q71FADBifunctional protein PutA/0.467
4ajp88NL-lactate dehydrogenase A chain1.1.1.270.466
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.466
1ma0NADAlcohol dehydrogenase class-31.1.1.10.465
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.465
2xlrFADPutative flavin-containing monooxygenase/0.465
1mp0NADAlcohol dehydrogenase class-31.1.1.10.464
1wzeNADMalate dehydrogenase/0.464
2oapANPType II secretion system protein (GspE-2)/0.464
3bhiNAPCarbonyl reductase [NADPH] 11.1.1.1840.463
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.463
1drhNAPDihydrofolate reductase1.5.1.30.462
1egeFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.462
3vdqNAD3-hydroxybutyrate dehydrogenase/0.462
4hwkNAPSepiapterin reductase1.1.1.1530.462
4i9h1E4L-lactate dehydrogenase A chain1.1.1.270.462
4z3dNDPCarbonyl reductase [NADPH] 11.1.1.1840.462
2emrSAHDiphthine synthase/0.461
3lqfNADGalactitol dehydrogenase/0.461
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.461
1q6t600Tyrosine-protein phosphatase non-receptor type 13.1.3.480.460
2ebaFADPutative glutaryl-CoA dehydrogenase/0.460
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.460
4fj0NAP17beta-hydroxysteroid dehydrogenase/0.460
2p83MR0Beta-secretase 13.4.23.460.459
2xhd7T9Glutamate receptor 2/0.459
2zbaZBATrichothecene 3-O-acetyltransferase/0.459
4g3jVNTLanosterol 14-alpha-demethylase/0.459
5jscFADPutative acyl-CoA dehydrogenase/0.459
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.458
1pr9NAPL-xylulose reductase1.1.1.100.458
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.458
2vwhNAPGlucose 1-dehydrogenase/0.458
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.458
3toxNAPPutative oxidoreductase/0.458
3w4yFADMitochondrial FAD-linked sulfhydryl oxidase ERV11.8.3.20.458
4q72FADBifunctional protein PutA/0.458
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.458
5idwNAPShort-chain dehydrogenase/reductase SDR/0.458
1d0mBLGMembrane-bound lytic murein transglycosylase B4.2.2.n10.457
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.457
1kkq471Peroxisome proliferator-activated receptor alpha/0.457
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.457
3nxxNDPDihydrofolate reductase1.5.1.30.457
4ambDUDPutative glycosyl transferase/0.457
1cf3FADGlucose oxidase1.1.3.40.456
2omeNADC-terminal-binding protein 2/0.456
3bv2P38Mitogen-activated protein kinase 14/0.456
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.456
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.456
4dbzNDPPutative ketoacyl reductase1.3.10.456
4dl9NADS-(hydroxymethyl)glutathione dehydrogenase/0.456
4fj2NAP17beta-hydroxysteroid dehydrogenase/0.456
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.456
4yxm2BADNA integrity scanning protein DisA/0.456
1xddAAYIntegrin alpha-L/0.455
2x0rNADMalate dehydrogenase/0.455
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.455
3zvmADPBifunctional polynucleotide phosphatase/kinase2.7.1.780.455
4ajj88RL-lactate dehydrogenase A chain1.1.1.270.455
4gk3L87Ephrin type-A receptor 32.7.10.10.455
4iqgNAPShort-chain dehydrogenase/reductase SDR/0.455
1w6hTITPlasmepsin-23.4.23.390.454
1yqdNAPSinapyl alcohol dehydrogenase/0.454
2v6gNAP3-oxo-Delta(4,5)-steroid 5-beta-reductase/0.454
1culFOKAdenylate cyclase type 2/0.453
1culFOKAdenylate cyclase type 5/0.453
1f8fNADBenzyl alcohol dehydrogenase/0.453
1qr6NADNAD-dependent malic enzyme, mitochondrial1.1.1.380.453
2gjlFMNNitronate monooxygenase1.13.12.160.453
2rabFADGlutathione amide reductase/0.453
3d3wNAPL-xylulose reductase1.1.1.100.453
3lsiFADPyranose 2-oxidase/0.453
3tjzGNPADP-ribosylation factor 1/0.453
3to6LYS_CMCHistone acetyltransferase ESA1/0.453
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.452
1mzs6693-oxoacyl-[acyl-carrier-protein] synthase 3/0.452
1qo8FADFumarate reductase flavoprotein subunit/0.452
1r2jFADFkbI/0.452
1v9aSAHUncharacterized protein/0.452
1yb5NAPQuinone oxidoreductase1.6.5.50.452
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.452
2e8qSAHDiphthine synthase/0.452
2igoFADPyranose 2-oxidase/0.452
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.452
2ou2ACOHistone acetyltransferase KAT5/0.452
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.452
3gw9VNILanosterol 14-alpha-demethylase/0.452
3hx4ANPCalmodulin-domain protein kinase 1/0.452
3kybFADUDP-galactopyranose mutase5.4.99.90.452
4eb5PLPCysteine desulfurase IscS 2/0.452
1kevNDPNADP-dependent isopropanol dehydrogenase1.1.1.800.451
1xe55FEPlasmepsin-23.4.23.390.451
2hdjNDPAldo-keto reductase family 1 member C2/0.451
2qo9ANPEphrin type-A receptor 32.7.10.10.451
3ms421NGlycogen phosphorylase, muscle form2.4.1.10.451
3qlsNDPDihydrofolate reductase1.5.1.30.451
3sx2NADUncharacterized protein/0.451
4c4oNADSADH/0.451
4d89BXDBeta-secretase 13.4.23.460.451
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.451
4xcvNDPProbable hydroxyacid dehydrogenase protein/0.451
4yryNADGlutamate synthase, beta subunit/0.451
5ahsFADAcyl-CoA dehydrogenase/0.451
5dcyNAPIridoid synthase1.3.1.990.451
1d4pBPPProthrombin3.4.21.50.450
1lquNDPNADPH-ferredoxin reductase FprA1.18.1.20.450
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.450
2dxvSAHDiphthine synthase/0.450
2eldSAHDiphthine synthase/0.450
2fj1CTCTetracycline repressor protein class D/0.450
2qbuSAHPrecorrin-2 methyltransferase/0.450
2x0iNAIMalate dehydrogenase/0.450
3cosNADAlcohol dehydrogenase 41.1.1.10.450
3f3sNADLambda-crystallin homolog/0.450
3lpiZ74Beta-secretase 13.4.23.460.450
3uleC69Actin-related protein 3/0.450
4an4DUDPutative glycosyl transferase/0.450
4jbiNDPAlcohol dehydrogenase (Zinc)/0.450
4udrFAD5-(hydroxymethyl)furfural oxidase/0.450
4z0g5GPInosine-5'-monophosphate dehydrogenase/0.450
1d0lBLGMembrane-bound lytic murein transglycosylase B4.2.2.n10.449
1me6IVSPlasmepsin-23.4.23.390.449
2q5g1FAPeroxisome proliferator-activated receptor delta/0.449
2y0mACOHistone acetyltransferase KAT8/0.449
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3hyoADPPyridoxal kinase/0.449
3ijrNADOxidoreductase, short chain dehydrogenase/reductase family/0.449
3kgcLY7Glutamate receptor 2/0.449
4g1cCNANAD-dependent protein deacylase sirtuin-5, mitochondrial/0.449
4ly91YYGlucokinase regulatory protein/0.449
2a87FADThioredoxin reductase1.8.1.90.448
2c29NAPDihydroflavonol 4-reductase/0.448
2ft9CHDFatty acid-binding protein 2, liver/0.448
3c1y2BADNA integrity scanning protein DisA/0.448
3fcjFADNitroalkane oxidase1.7.3.10.448
3mt817TGlycogen phosphorylase, muscle form2.4.1.10.448
3tscNADUncharacterized protein/0.448
4ef8FMNDihydroorotate dehydrogenase (fumarate)/0.448
1fxsNAPGDP-L-fucose synthase/0.447
1h74ADPHomoserine kinase2.7.1.390.447
1kvkATPMevalonate kinase2.7.1.360.447
1rneC60Renin3.4.23.150.447
1yqxNAPSinapyl alcohol dehydrogenase/0.447
2gcgNDPGlyoxylate reductase/hydroxypyruvate reductase1.1.1.790.447
2hk9NAPShikimate dehydrogenase (NADP(+))/0.447
2pb4SAHDiphthine synthase/0.447
2pcmSAHDiphthine synthase/0.447
2ylxFADPhenylacetone monooxygenase1.14.13.920.447
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.447
3uylTYDProbable NDP-rhamnosyltransferase/0.447
4eb7PLPCysteine desulfurase IscS 2/0.447
4r81FMNPredicted NADH dehydrogenase/0.447
4twrNADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase/0.447
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.447
5a3bAPRSIR2 family protein/0.447
1ai9NDPDihydrofolate reductase1.5.1.30.446
1sq5ADPPantothenate kinase2.7.1.330.446
1wziNDPMalate dehydrogenase/0.446
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.446
2vbpVB1Isopenicillin N synthase1.21.3.10.446
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4fue7UPUrokinase-type plasminogen activator3.4.21.730.446
4rvfTYDD-mycarose 3-C-methyltransferase/0.446
4yerADPAntibiotic ABC transporter, ATP-binding protein, putative/0.446
5jsfNAD17-beta-hydroxysteroid dehydrogenase 141.1.10.446
1eq2NAPADP-L-glycero-D-manno-heptose-6-epimerase/0.445
1gsnFADGlutathione reductase, mitochondrial1.8.1.70.445
1mg5NAIAlcohol dehydrogenase1.1.1.10.445
1pj3NADNAD-dependent malic enzyme, mitochondrial1.1.1.380.445
1tdeFADThioredoxin reductase1.8.1.90.445
1zmcNADDihydrolipoyl dehydrogenase, mitochondrial1.8.1.40.445
2dsgSAHDiphthine synthase/0.445
2gsdNADFormate dehydrogenase/0.445
2qn3F55Glycogen phosphorylase, muscle form2.4.1.10.445
2qn7HBZGlycogen phosphorylase, muscle form2.4.1.10.445
2v3oI26Prothrombin3.4.21.50.445
3dmeFADPutative conserved exported protein/0.445
3lpkZ76Beta-secretase 13.4.23.460.445
3pefNAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase/0.445
4a87NARMajor pollen allergen Bet v 1-A/0.445
4dh60KNBeta-secretase 13.4.23.460.445
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.445
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.445
4j7uNAPSepiapterin reductase1.1.1.1530.445
1e3eNAIAlcohol dehydrogenase 41.1.1.10.444
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.444
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.444
1rwbNADGlucose 1-dehydrogenase1.1.1.470.444
1y7lASN_LEU_ASN_ILECysteine synthase2.5.1.470.444
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.444
2ywlFADThioredoxin reductase related protein/0.444
3ig6438Urokinase-type plasminogen activator3.4.21.730.444
3il1B5DGlutamate receptor 2/0.444
3k5gBJCBeta-secretase 13.4.23.460.444
3t2zFADSulfide-quinone reductase/0.444
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.444
4b1bFADThioredoxin reductase1.8.1.90.444
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.444
4nbwNADShort-chain dehydrogenase/reductase SDR/0.444
4p9dTMPDeoxycytidylate deaminase/0.444
4yaiNAIC alpha-dehydrogenase/0.444
1ae1NAPTropinone reductase 1/0.443
1bdbNADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase/0.443
1bdmNAXMalate dehydrogenase/0.443
1hdoNAPFlavin reductase (NADPH)/0.443
1n2sNAIdTDP-4-dehydrorhamnose reductase1.1.1.1330.443
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.443
1udaUFGUDP-glucose 4-epimerase5.1.3.20.443
1w5tANPORC1-type DNA replication protein 2/0.443
2ejjSAHDiphthine synthase/0.443
2j09FMNDeoxyribodipyrimidine photo-lyase4.1.99.30.443
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.443
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
4eu8COASuccinyl-CoA:acetate CoA-transferase/0.443
4n3cUD1UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.443
4xd2NAIAlcohol dehydrogenase E chain1.1.1.10.443
1okkGCPSignal recognition particle protein/0.442
1okkGCPSignal recognition particle receptor FtsY/0.442
2c27ACOMycothiol acetyltransferase2.3.1.1890.442
2en5SAHDiphthine synthase/0.442
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
2gdzNAD15-hydroxyprostaglandin dehydrogenase [NAD(+)]1.1.1.1410.442
2hr8SAHDiphthine synthase/0.442
2iviACWIsopenicillin N synthase1.21.3.10.442
2p5fSAHDiphthine synthase/0.442
3a4vNADNDP-sugar epimerase/0.442
3autNAIGlucose 1-dehydrogenase 41.1.1.470.442
3c1kT15Prothrombin3.4.21.50.442
3ensENSCoagulation factor X3.4.21.60.442
3oibFDAPutative acyl-CoA dehydrogenase/0.442
3wleNAD(R)-specific carbonyl reductase/0.442
4dd8BATDisintegrin and metalloproteinase domain-containing protein 83.4.240.442
4xnhACON-terminal acetyltransferase A complex subunit NAT52.3.10.442
5kjcNAJAlcohol dehydrogenase E chain1.1.1.10.442
5l3dFADLysine-specific histone demethylase 1A10.442
1b8uNADMalate dehydrogenase/0.441
1j1zATPArgininosuccinate synthase/0.441
1mjbACOHistone acetyltransferase ESA1/0.441
1y7tNDPMalate dehydrogenase/0.441
1ykfNAPNADP-dependent isopropanol dehydrogenase1.1.1.800.441
1z4uPH9Polyprotein/0.441
3ak4NADNADH-dependent quinuclidinone reductase/0.441
3gy0NAPNAD(P)-dependent oxidoreductase/0.441
3jv7NADSecondary alcohol dehydrogenase/0.441
3zbsOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.441
4bkqNAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.441
4bmsNAPAlclohol dehydrogenase/short-chain dehydrogenase/0.441
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.441
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1k8cNAPNAD(P)H-dependent D-xylose reductase1.1.1.3070.440
1n5dNDPCarbonyl reductase [NADPH] 1/0.440
1obnASVIsopenicillin N synthase1.21.3.10.440
2bi8FADUDP-galactopyranose mutase5.4.99.90.440
2dteNAIGlucose 1-dehydrogenase related protein/0.440
3mpt1GKMitogen-activated protein kinase 14/0.440
3ndrNADPyridoxal 4-dehydrogenase1.1.1.1070.440
3p19NDPPutative blue fluorescent protein/0.440
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.440
3v2uATPProtein GAL3/0.440
4blsAPCNTPase P4/0.440
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.440
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.440
4egbNADdTDP-glucose 4,6-dehydratase/0.440
4ejmNAPPutative zinc-binding dehydrogenase/0.440
4frkDWDBeta-secretase 13.4.23.460.440
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.440
4uocNCNCinA-like protein/0.440
4weqNAPNAD-dependent dehydrogenase/0.440
5dbgNADIridoid synthase1.3.1.990.440