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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
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/1.000
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.757
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.680
4nd4NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.642
2a94AP0L-lactate dehydrogenase1.1.1.270.581
2a92NAIL-lactate dehydrogenase/0.567
1t2cNAIL-lactate dehydrogenase1.1.1.270.561
2aa3AP0L-lactate dehydrogenase/0.542
4rosAPRMalate dehydrogenase/0.535
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.531
3gvhNADMalate dehydrogenase/0.530
1guyNADMalate dehydrogenase/0.517
1ur5NADMalate dehydrogenase/0.513
1uxjNADMalate dehydrogenase/0.511
1uxkNADMalate dehydrogenase/0.510
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.508
1pzgA3DLactate dehydrogenase/0.507
1pzhNADLactate dehydrogenase/0.506
4nbwNADShort-chain dehydrogenase/reductase SDR/0.505
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.504
4i1iNADMalate dehydrogenase/0.503
1sowNADL-lactate dehydrogenase1.1.1.270.501
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.500
4mdhNADMalate dehydrogenase, cytoplasmic1.1.1.370.499
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.497
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.496
4egbNADdTDP-glucose 4,6-dehydratase/0.496
1ie3NADMalate dehydrogenase/0.494
3lqfNADGalactitol dehydrogenase/0.493
2i4qUA4Renin3.4.23.150.490
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.490
4yaoFMNNADPH--cytochrome P450 reductase/0.490
2g247IGRenin3.4.23.150.489
1pzfA3DLactate dehydrogenase/0.488
2g226IGRenin3.4.23.150.488
4qecNAPElxO/0.487
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.484
4lcjNADC-terminal-binding protein 2/0.484
4q71FADBifunctional protein PutA/0.484
2g1o2IGRenin3.4.23.150.483
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.481
3b70NAPEnoyl reductase LovC10.481
4l4sNAIL-lactate dehydrogenase A chain1.1.1.270.481
1qlhNADAlcohol dehydrogenase E chain1.1.1.10.480
2iko7IGRenin3.4.23.150.480
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.479
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.479
1ez4NADL-lactate dehydrogenase1.1.1.270.477
4dbzNDPPutative ketoacyl reductase1.3.10.477
5mdhNADMalate dehydrogenase, cytoplasmic1.1.1.370.477
1tehNADAlcohol dehydrogenase class-31.1.1.10.476
1xddAAYIntegrin alpha-L/0.476
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.476
1b2lNDCAlcohol dehydrogenase1.1.1.10.475
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.475
3tjzGNPADP-ribosylation factor 1/0.475
5a3bAPRSIR2 family protein/0.475
1xe55FEPlasmepsin-23.4.23.390.474
2gcgNDPGlyoxylate reductase/hydroxypyruvate reductase1.1.1.790.474
2dftADPShikimate kinase2.7.1.710.473
2g1r3IGRenin3.4.23.150.473
1g1aNADdTDP-glucose 4,6-dehydratase/0.472
1rneC60Renin3.4.23.150.472
3qlsNDPDihydrofolate reductase1.5.1.30.472
4eudCOASuccinyl-CoA:acetate CoA-transferase/0.472
4g7gVFVLanosterol 14-alpha-demethylase/0.472
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.471
3b6zCO7Enoyl reductase LovC10.471
3ekuCY9Actin-5C/0.471
3gqvNAPEnoyl reductase LovC10.471
4dc0NDPPutative ketoacyl reductase1.3.10.471
4g74FADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.471
3a3gDLZLumazine protein/0.470
4gl4NAIAlcohol dehydrogenase class-3/0.470
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.469
5d3qGDPDynamin-13.6.5.50.469
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.468
3gviADPMalate dehydrogenase/0.468
3d4pNADL-lactate dehydrogenase 11.1.1.270.467
3wswNADL-lactate dehydrogenase/0.467
4eu8COASuccinyl-CoA:acetate CoA-transferase/0.467
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.466
3h3fNAIL-lactate dehydrogenase A chain1.1.1.270.466
3kb1ADPIron-sulfur cluster carrier protein/0.466
4blsAPCNTPase P4/0.466
4rlsNAIL-lactate dehydrogenase A chain1.1.1.270.466
3uylTYDProbable NDP-rhamnosyltransferase/0.465
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.465
2dc1NADProbable L-aspartate dehydrogenase/0.464
2givACOHistone acetyltransferase KAT8/0.464
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.464
4ejmNAPPutative zinc-binding dehydrogenase/0.464
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.464
4m6jNDPDihydrofolate reductase1.5.1.30.464
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.464
1hyhNADL-2-hydroxyisocaproate dehydrogenase/0.463
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.463
2ft9CHDFatty acid-binding protein 2, liver/0.463
2rcyNAPPyrroline-5-carboxylate reductase/0.463
2x0iNAIMalate dehydrogenase/0.463
2y0mACOHistone acetyltransferase KAT8/0.463
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.463
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.462
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.462
2ou2ACOHistone acetyltransferase KAT5/0.462
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.462
3toxNAPPutative oxidoreductase/0.462
4m83ERYOleandomycin glycosyltransferase2.4.10.462
1pjcNADAlanine dehydrogenase/0.461
2g1s4IGRenin3.4.23.150.461
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.461
3h3jNADL-lactate dehydrogenase 11.1.1.270.461
4g3jVNTLanosterol 14-alpha-demethylase/0.461
1emdNADMalate dehydrogenase/0.460
1f8fNADBenzyl alcohol dehydrogenase/0.460
1gpdNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.460
1h50FMNPentaerythritol tetranitrate reductase/0.460
1udbUFGUDP-glucose 4-epimerase5.1.3.20.460
2omeNADC-terminal-binding protein 2/0.460
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.460
3d3wNAPL-xylulose reductase1.1.1.100.460
3ensENSCoagulation factor X3.4.21.60.460
4bkqNAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.460
4usqFADPyridine nucleotide-disulfide oxidoreductase/0.460
4z3dNDPCarbonyl reductase [NADPH] 11.1.1.1840.460
5a3cNADSIR2 family protein/0.460
1ia1NDPDihydrofolate reductase1.5.1.30.459
2ejvNADL-threonine 3-dehydrogenase/0.459
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.459
3nsh957Beta-secretase 13.4.23.460.459
4hwkNAPSepiapterin reductase1.1.1.1530.459
4i0i957Beta-secretase 13.4.23.460.459
4q73FADBifunctional protein PutA/0.459
4udrFAD5-(hydroxymethyl)furfural oxidase/0.459
2gjlFMNNitronate monooxygenase1.13.12.160.458
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.458
4eb7PLPCysteine desulfurase IscS 2/0.458
1fy7COAHistone acetyltransferase ESA1/0.457
1xkdNAPIsocitrate dehydrogenase [NADP]/0.457
2g1y5IGRenin3.4.23.150.457
2p5uNADUDP-glucose 4-epimerase/0.457
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.457
3mk6ACOPantothenate kinase 32.7.1.330.457
3rucNADUDP-N-acetylglucosamine 4-epimerase/0.457
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.457
1eioGCHGastrotropin/0.456
1h73ANPHomoserine kinase2.7.1.390.456
1u3dFADCryptochrome-1/0.456
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.456
3gw9VNILanosterol 14-alpha-demethylase/0.456
3ruaNADUDP-N-acetylglucosamine 4-epimerase/0.456
3vsxR32Renin3.4.23.150.456
4k6fNAPPutative Acetoacetyl-CoA reductase/0.456
1lbcCYZGlutamate receptor 2/0.455
1me6IVSPlasmepsin-23.4.23.390.455
2gv8NDPThiol-specific monooxygenase1.14.130.455
2he5NDPAldo-keto reductase family 1 member C211.1.10.455
2ignFADPyranose 2-oxidase/0.455
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.455
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.455
8dfrNDPDihydrofolate reductase1.5.1.30.455
1b8uNADMalate dehydrogenase/0.454
1g6kNADGlucose 1-dehydrogenase1.1.1.470.454
2h9iEADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
2ifaFMNUncharacterized protein/0.454
3lu1NADUDP-N-acetylglucosamine 4-epimerase/0.454
4ambDUDPutative glycosyl transferase/0.454
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.454
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.454
5fm7ADPRuvB-like helicase/0.454
2c29NAPDihydroflavonol 4-reductase/0.453
3bg7FADPyranose 2-oxidase/0.453
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.453
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.453
3nxxNDPDihydrofolate reductase1.5.1.30.453
3r6sCMPCRP-like cAMP-activated global transcriptional regulator/0.453
4rvfTYDD-mycarose 3-C-methyltransferase/0.453
4rvgTYDD-mycarose 3-C-methyltransferase/0.453
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.453
2ikuLIYRenin3.4.23.150.452
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.452
1xnyBTNPropionyl-CoA carboxylase complex B subunit/0.451
2il2LIXRenin3.4.23.150.451
2ylrNAPPhenylacetone monooxygenase1.14.13.920.451
2zb3NDPProstaglandin reductase 21.3.1.480.451
3btsNADGalactose/lactose metabolism regulatory protein GAL80/0.451
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.451
3oqfS51Renin3.4.23.150.451
3qe2FMNNADPH--cytochrome P450 reductase/0.451
4fse0VABeta-secretase 13.4.23.460.451
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.450
3sj7NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative/0.450
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.450
4dreNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.450
4q0kGA3Phytohormone-binding protein/0.450
1ma0NADAlcohol dehydrogenase class-31.1.1.10.449
1mjbACOHistone acetyltransferase ESA1/0.449
2fy4COACholine O-acetyltransferase2.3.1.60.449
2rlcCHDCholoylglycine hydrolase3.5.1.240.449
3ai2NDPNADPH-sorbose reductase/0.449
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.449
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3ieuGDPGTPase Era/0.449
1fm4DXCMajor pollen allergen Bet v 1-L/0.448
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.448
1xvaSAMGlycine N-methyltransferase2.1.1.200.448
2b53D23Cyclin-dependent kinase 22.7.11.220.448
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.448
2yylFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.448
3ijrNADOxidoreductase, short chain dehydrogenase/reductase family/0.448
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.448
3lpiZ74Beta-secretase 13.4.23.460.448
3rpeFADPutative modulator of drug activity/0.448
3sglFADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC/0.448
3v2uATPProtein GAL3/0.448
3vyfVYFRenin3.4.23.150.448
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.448
4r81FMNPredicted NADH dehydrogenase/0.448
5jsfNAD17-beta-hydroxysteroid dehydrogenase 141.1.10.448
1gv0NADMalate dehydrogenase/0.447
1x1aSAMC-20 methyltransferase/0.447
2hsdNAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.447
2ohvNHLGlutamate racemase/0.447
3tscNADUncharacterized protein/0.447
3vyeVYERenin3.4.23.150.447
4f4qFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.447
4mlp2CXCryptochrome-2/0.447
4xguADPPutative pachytene checkpoint protein 2/0.447
1mj9COAHistone acetyltransferase ESA1/0.446
1x27ASP_TYR_VAL_HIS_PTRTyrosine-protein kinase Lck2.7.10.20.446
1ykfNAPNADP-dependent isopropanol dehydrogenase1.1.1.800.446
2igoFADPyranose 2-oxidase/0.446
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.446
2wdzNADGalactitol dehydrogenase/0.446
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.446
3ai3NDPNADPH-sorbose reductase/0.446
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3hl0NADMaleylacetate reductase/0.446
3mvm39PMitogen-activated protein kinase 14/0.446
3oqkS52Renin3.4.23.150.446
4kwhNAPReductase homolog/0.446
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.445
2c12FADNitroalkane oxidase1.7.3.10.445
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.445
3jzdNADMaleylacetate reductase/0.445
3k4nFADPyranose 2-oxidase/0.445
3w8eNAD3-hydroxybutyrate dehydrogenase/0.445
4dfg0JVGag-Pol polyprotein3.4.23.160.445
4loi1YCStimulator of interferon genes protein/0.445
4tuvCPZCytochrome P450 1191.140.445
4yaiNAIC alpha-dehydrogenase/0.445
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.445
1mjaCOAHistone acetyltransferase ESA1/0.444
1w6hTITPlasmepsin-23.4.23.390.444
2a7r5GPGMP reductase 2/0.444
2oapANPType II secretion system protein (GspE-2)/0.444
2vnaNAPProstaglandin reductase 21.3.1.480.444
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.444
3nutSAHPrecorrin-3 methylase/0.444
3pw8ACO1,2-phenylacetyl-CoA epoxidase, subunit A1.14.13.1490.444
3qlrNDPDihydrofolate reductase1.5.1.30.444
3sufSUEPolyprotein/0.444
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.444
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.444
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.444
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.443
2djxFMNDihydroorotate dehydrogenase (fumarate)1.3.98.10.443
2ien017Gag-Pol polyprotein3.4.23.160.443
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.443
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.443
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.443
2zvbSAHPrecorrin-3 C17-methyltransferase/0.443
3hbbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
3ruhNADUDP-N-acetylglucosamine 4-epimerase/0.443
3w8wFADPutative FAD-dependent oxygenase EncM/0.443
4df2FMNNADPH dehydrogenase/0.443
4yxm2BADNA integrity scanning protein DisA/0.443
5jlaNADPutative short-chain dehydrogenase/reductase/0.443
5jscFADPutative acyl-CoA dehydrogenase/0.443
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.442
2c27ACOMycothiol acetyltransferase2.3.1.1890.442
2ozuACOHistone acetyltransferase KAT6A/0.442
2uxoTACHTH-type transcriptional regulator TtgR/0.442
2vjmCOAFormyl-CoA:oxalate CoA-transferase/0.442
2y3rTRKTamL/0.442
3f63GTXGlutathione transferase GST1-4/0.442
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.442
3qt62P0Mevalonate diphosphate decarboxylase/0.442
3syiFADSulfide-quinone reductase/0.442
3zc3NAPFerredoxin--NADP reductase1.18.1.20.442
4ej0NAPADP-L-glycero-D-manno-heptose-6-epimerase/0.442
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.442
4jx1CAHCamphor 5-monooxygenase1.14.15.10.442
4ktoFADPutative isovaleryl-CoA dehydrogenase protein/0.442
1bil0IURenin3.4.23.150.441
1gqtACPRibokinase/0.441
1ib6NADMalate dehydrogenase/0.441
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.441
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.441
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.441
3e8xNAPBH1520 protein/0.441
3f1kNAPUncharacterized oxidoreductase YciK10.441
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.441
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.441
3ohh3HHBeta-secretase 13.4.23.460.441
4ajj88RL-lactate dehydrogenase A chain1.1.1.270.441
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
5dp2NAPCurF/0.441
5idwNAPShort-chain dehydrogenase/reductase SDR/0.441
1ae1NAPTropinone reductase 1/0.440
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.440
1jioDEB6-deoxyerythronolide B hydroxylase/0.440
1mp0NADAlcohol dehydrogenase class-31.1.1.10.440
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.440
2nniMTKCytochrome P450 2C8/0.440
3to6LYS_CMCHistone acetyltransferase ESA1/0.440
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.440
4jicFMNGTN Reductase/0.440
4oqyNDP(S)-imine reductase/0.440
5ftfADPTPR domain protein/0.440
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.440