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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
4ajj88RL-lactate dehydrogenase A chain1.1.1.27

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4ajj88RL-lactate dehydrogenase A chain1.1.1.271.000
4ajn88VL-lactate dehydrogenase A chain1.1.1.270.674
4ajo88NL-lactate dehydrogenase A chain1.1.1.270.608
4al4W7EL-lactate dehydrogenase A chain1.1.1.270.569
3h3jNADL-lactate dehydrogenase 11.1.1.270.555
2x0iNAIMalate dehydrogenase/0.534
3h3fNAIL-lactate dehydrogenase A chain1.1.1.270.533
2a94AP0L-lactate dehydrogenase1.1.1.270.528
1ez4NADL-lactate dehydrogenase1.1.1.270.517
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.508
4rosAPRMalate dehydrogenase/0.504
1pzgA3DLactate dehydrogenase/0.496
1sowNADL-lactate dehydrogenase1.1.1.270.490
4du82P0Mevalonate diphosphate decarboxylase/0.490
1ib6NADMalate dehydrogenase/0.489
3gvhNADMalate dehydrogenase/0.488
3uylTYDProbable NDP-rhamnosyltransferase/0.487
1dyjDDFDihydrofolate reductase1.5.1.30.481
1t2cNAIL-lactate dehydrogenase1.1.1.270.481
3kb6NADD-lactate dehydrogenase/0.481
4k28NADShikimate dehydrogenase family protein/0.481
4l4sNAIL-lactate dehydrogenase A chain1.1.1.270.478
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.478
2zbaZBATrichothecene 3-O-acetyltransferase/0.477
4dpuAGSMevalonate diphosphate decarboxylase/0.477
1v9aSAHUncharacterized protein/0.474
3qw4U5POrotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative/0.474
1nzfUPGDNA beta-glucosyltransferase/0.473
1pzhNADLactate dehydrogenase/0.472
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.472
3qt62P0Mevalonate diphosphate decarboxylase/0.472
4dbzNDPPutative ketoacyl reductase1.3.10.472
4r1lADPPhenylacetate-coenzyme A ligase/0.472
4cr8NADN-acylmannosamine 1-dehydrogenase1.1.1.2330.471
4xb2NDP319aa long hypothetical homoserine dehydrogenase/0.471
1u5aBIKL-lactate dehydrogenase1.1.1.270.470
4ie6UN9Alpha-ketoglutarate-dependent dioxygenase FTO/0.470
1pzfA3DLactate dehydrogenase/0.469
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.469
1dr3TAPDihydrofolate reductase1.5.1.30.468
1h51FMNPentaerythritol tetranitrate reductase/0.468
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.468
2q61SF1Peroxisome proliferator-activated receptor gamma/0.468
2qfxNDPIsocitrate dehydrogenase [NADP], mitochondrial1.1.1.420.468
4j7uNAPSepiapterin reductase1.1.1.1530.468
4m4922YL-lactate dehydrogenase A chain1.1.1.270.468
1g4tFTPThiamine-phosphate synthase/0.467
1ie3NADMalate dehydrogenase/0.467
2x0rNADMalate dehydrogenase/0.467
2ydxNAPMethionine adenosyltransferase 2 subunit beta/0.467
3bv2P38Mitogen-activated protein kinase 14/0.467
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.467
4q71FADBifunctional protein PutA/0.467
5a3bAPRSIR2 family protein/0.467
1dr3HBIDihydrofolate reductase1.5.1.30.466
1emdNADMalate dehydrogenase/0.466
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.466
2y5s78HDihydropteroate synthase/0.466
3p62FMNPentaerythritol tetranitrate reductase/0.466
1dliUDXUDP-glucose 6-dehydrogenase/0.465
2oapANPType II secretion system protein (GspE-2)/0.465
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.465
2znpK55Peroxisome proliferator-activated receptor delta/0.464
3b9lAZZSerum albumin/0.464
4i8x6P3L-lactate dehydrogenase A chain1.1.1.270.464
1pd9CO4Dihydrofolate reductase1.5.1.30.463
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.463
2vbpVB1Isopenicillin N synthase1.21.3.10.463
4dfrMTXDihydrofolate reductase1.5.1.30.463
1ipeNDPTropinone reductase 21.1.1.2360.462
1omoNADAlanine dehydrogenase/0.462
2wo7ASVIsopenicillin N synthase1.21.3.10.462
4rf2NAPNADPH dependent R-specific alcohol dehydrogenase/0.462
1dyhDZFDihydrofolate reductase1.5.1.30.461
1y57MPZProto-oncogene tyrosine-protein kinase Src2.7.10.20.461
3a1nNADNDP-sugar epimerase/0.461
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.461
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.461
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.460
1bsvNDPGDP-L-fucose synthase/0.459
1dhiMTXDihydrofolate reductase1.5.1.30.459
2a92NAIL-lactate dehydrogenase/0.459
3lqfNADGalactitol dehydrogenase/0.459
1yjqNAP2-dehydropantoate 2-reductase1.1.1.1690.458
2e0nSAHPrecorrin-2 C20-methyltransferase/0.458
4kwhNAPReductase homolog/0.458
4x9mFADUncharacterized protein MG039 homolog/0.458
1qr6NADNAD-dependent malic enzyme, mitochondrial1.1.1.380.457
1udbUFGUDP-glucose 4-epimerase5.1.3.20.457
3fwjCAMCamphor 5-monooxygenase1.14.15.10.457
4j7xNAPSepiapterin reductase1.1.1.1530.457
1qjfACSIsopenicillin N synthase1.21.3.10.456
1udaUFGUDP-glucose 4-epimerase5.1.3.20.456
1xddAAYIntegrin alpha-L/0.456
2q9fC3SCholesterol 24-hydroxylase/0.456
3bhiNAPCarbonyl reductase [NADPH] 11.1.1.1840.456
3o26NDPSalutaridine reductase/0.456
4e5mNAPPhosphonate dehydrogenase1.20.1.10.456
4ipw1G7Mycocyclosin synthase1.14.21.90.456
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.456
4yagNAIC alpha-dehydrogenase/0.456
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.455
1jolFFODihydrofolate reductase1.5.1.30.455
1vl8NAPOxidoreductase, short chain dehydrogenase/reductase family/0.455
1zeoC01Peroxisome proliferator-activated receptor gamma/0.455
2p5uNADUDP-glucose 4-epimerase/0.455
2ww4ADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.455
2y8lADP5'-AMP-activated protein kinase subunit gamma-1/0.455
3umpATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.455
4gk3L87Ephrin type-A receptor 32.7.10.10.455
4lb2DM5Serum albumin/0.455
5d3qGDPDynamin-13.6.5.50.455
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.454
2o23NAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.454
2q2qNADBeta-D-hydroxybutyrate dehydrogenase/0.454
2qbmCAMCamphor 5-monooxygenase1.14.15.10.454
2r9eSDXCitrate synthase2.3.3.160.454
2vbdV10Isopenicillin N synthase1.21.3.10.454
2y6fM9FIsopenicillin N synthase1.21.3.10.454
2yltNAPPhenylacetone monooxygenase1.14.13.920.454
3il1B5DGlutamate receptor 2/0.454
3toxNAPPutative oxidoreductase/0.454
5fklTDCTetracycline repressor protein class D/0.454
1kkq471Peroxisome proliferator-activated receptor alpha/0.453
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.453
2ylrNAPPhenylacetone monooxygenase1.14.13.920.453
3gluLYS_VAL_METNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.453
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
4bfxZVXPantothenate kinase2.7.1.330.453
4q72FADBifunctional protein PutA/0.453
1kvsUPGUDP-glucose 4-epimerase5.1.3.20.452
1orrNADCDP-paratose 2-epimerase/0.452
2balPQAMitogen-activated protein kinase 14/0.452
3d3wNAPL-xylulose reductase1.1.1.100.452
3nmpPYVAbscisic acid receptor PYL2/0.452
1xelUPGUDP-glucose 4-epimerase5.1.3.20.451
2aa3AP0L-lactate dehydrogenase/0.451
2eklNADD-3-phosphoglycerate dehydrogenase/0.451
2qo9ANPEphrin type-A receptor 32.7.10.10.451
2vcmM11Isopenicillin N synthase1.21.3.10.451
3nxxNDPDihydrofolate reductase1.5.1.30.451
4b8wNAPGDP-L-fucose synthase1.1.1.2710.451
4o0lNDPNADPH-dependent 3-quinuclidinone reductase/0.451
1kt8ILPBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.450
1obnASVIsopenicillin N synthase1.21.3.10.450
2bunFADAppA protein/0.450
2givACOHistone acetyltransferase KAT8/0.450
3b2sB2STrichothecene 3-O-acetyltransferase/0.450
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.450
5jlaNADPutative short-chain dehydrogenase/reductase/0.450
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
1ytmATPPhosphoenolpyruvate carboxykinase (ATP)/0.449
2g5cNADPrephenate dehydrogenase/0.449
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.449
3w8eNAD3-hydroxybutyrate dehydrogenase/0.449
4bfsZVSPantothenate kinase2.7.1.330.449
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.448
1bdlIM1Gag-Pol polyprotein3.4.23.160.448
1pq944BOxysterols receptor LXR-beta/0.448
1rx8NAPDihydrofolate reductase1.5.1.30.448
2dbzNAPGlyoxylate reductase1.1.1.260.448
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.448
2qenADPWalker-Type ATPase/0.448
3zkyWT4Isopenicillin N synthase1.21.3.10.448
4bfvZVVPantothenate kinase2.7.1.330.448
4g95OAGDihydrofolate reductase1.5.1.30.448
4i8vBHFCytochrome P450 1A11.14.14.10.448
4yerADPAntibiotic ABC transporter, ATP-binding protein, putative/0.448
1a9yUPGUDP-glucose 4-epimerase5.1.3.20.447
1m2qMNXCasein kinase II subunit alpha2.7.11.10.447
1o76CAMCamphor 5-monooxygenase1.14.15.10.447
1o9bNAIQuinate/shikimate dehydrogenase/0.447
2fr0NDP6-deoxyerythronolide-B synthase EryA1, modules 1 and 2/0.447
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.447
2y8qADP5'-AMP-activated protein kinase subunit gamma-1/0.447
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.447
3uqdADPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.447
4d0l093Phosphatidylinositol 4-kinase beta2.7.1.670.447
4hwkNAPSepiapterin reductase1.1.1.1530.447
1h63FMNPentaerythritol tetranitrate reductase/0.446
1lbcCYZGlutamate receptor 2/0.446
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.446
2geuCOKPantothenate kinase2.7.1.330.446
2wpxACOOrf14/0.446
2yyuC5POrotidine 5'-phosphate decarboxylase/0.446
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.446
3gkaFMNN-ethylmaleimide reductase/0.446
3gwfFADCyclohexanone monooxygenase/0.446
4co4ATPNitrogen regulatory protein P-II 1/0.446
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.446
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.446
1ae1NAPTropinone reductase 1/0.445
1cjkFOKAdenylate cyclase type 2/0.445
1cjkFOKAdenylate cyclase type 5/0.445
1gebCAMCamphor 5-monooxygenase1.14.15.10.445
1t2dNADL-lactate dehydrogenase1.1.1.270.445
2a1nCAMCamphor 5-monooxygenase1.14.15.10.445
2gesCOKPantothenate kinase2.7.1.330.445
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.445
2rcyNAPPyrroline-5-carboxylate reductase/0.445
2w3bNDPDihydrofolate reductase1.5.1.30.445
2xpvMIYTetracycline repressor protein class D/0.445
3t4eNADQuinate/shikimate dehydrogenase/0.445
1g0nNDPTetrahydroxynaphthalene reductase1.1.1.2520.444
1hb3SCVIsopenicillin N synthase1.21.3.10.444
1snyNAPLD36273p/0.444
1t87CAMCamphor 5-monooxygenase1.14.15.10.444
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.444
2d29FADAcyl-CoA dehydrogenase/0.444
2dteNAIGlucose 1-dehydrogenase related protein/0.444
2gmvPEPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.444
2iviACWIsopenicillin N synthase1.21.3.10.444
2npxFADNADH peroxidase1.11.1.10.444
3bm1FMNPutative NAD(P)H nitroreductase YdjA/0.444
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.444
3iphG11Mitogen-activated protein kinase 14/0.444
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.444
4h8nNDPNADPH-dependent conjugated polyketone reductase C2/0.444
1b8uNADMalate dehydrogenase/0.443
1cydNDPCarbonyl reductase [NADPH] 21.1.1.1840.443
1ma0NADAlcohol dehydrogenase class-31.1.1.10.443
1t88CAMCamphor 5-monooxygenase1.14.15.10.443
1xe55FEPlasmepsin-23.4.23.390.443
2ejvNADL-threonine 3-dehydrogenase/0.443
2hfuMEVMevalonate kinase/0.443
2j2pSC2Ficolin-2/0.443
2nniMTKCytochrome P450 2C8/0.443
2v5aLZLBiotin carboxylase6.3.4.140.443
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.443
2xvv9DNSerum albumin/0.443
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.443
2znq401Peroxisome proliferator-activated receptor delta/0.443
3inmNDPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.443
3lsiFADPyranose 2-oxidase/0.443
3okxSAMS-adenosyl-L-methionine-binding protein RPA0152/0.443
3p82FMNPentaerythritol tetranitrate reductase/0.443
3ut5LOCTubulin beta chain/0.443
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
4fizCUE17beta-hydroxysteroid dehydrogenase/0.443
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.443
4ikeADPAdenylate kinase/0.443
4tuvCPZCytochrome P450 1191.140.443
4xgxADPFAD:protein FMN transferase/0.443
5idwNAPShort-chain dehydrogenase/reductase SDR/0.443
1adfTADAlcohol dehydrogenase E chain1.1.1.10.442
1b5dDCMDeoxycytidylate 5-hydroxymethyltransferase2.1.2.80.442
1dyiFOLDihydrofolate reductase1.5.1.30.442
1h65GDPTranslocase of chloroplast 343.6.50.442
1ur5NADMalate dehydrogenase/0.442
2abbFMNPentaerythritol tetranitrate reductase/0.442
2p5cSAHDiphthine synthase/0.442
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.442
3bbrBHYGlutamate receptor 2/0.442
3dufR1TPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.442
3dufR1TPyruvate dehydrogenase E1 component subunit beta1.2.4.10.442
3gviADPMalate dehydrogenase/0.442
3ojlNADCap5O/0.442
3p8jFMNPentaerythritol tetranitrate reductase/0.442
3tjzGNPADP-ribosylation factor 1/0.442
4dx7DM2Multidrug efflux pump subunit AcrB/0.442
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.442
1b8vNADMalate dehydrogenase/0.441
1bk0ACVIsopenicillin N synthase1.21.3.10.441
1h74ADPHomoserine kinase2.7.1.390.441
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1pjcNADAlanine dehydrogenase/0.441
1qr0COA4'-phosphopantetheinyl transferase sfp2.7.80.441
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.441
1uxjNADMalate dehydrogenase/0.441
1v0jFADUDP-galactopyranose mutase5.4.99.90.441
1x8lOXRRetinol dehydratase/0.441
2b7aIZATyrosine-protein kinase JAK2/0.441
2dc1NADProbable L-aspartate dehydrogenase/0.441
2drcMTXDihydrofolate reductase1.5.1.30.441
2ooyATP5'-AMP-activated protein kinase subunit gamma/0.441
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.441
2ya3J7V5'-AMP-activated protein kinase subunit gamma-1/0.441
3jzdNADMaleylacetate reductase/0.441
3mgdACOPredicted acetyltransferase/0.441
3n0z3ATAdenylate cyclase 2/0.441
3nr4PYVAbscisic acid receptor PYL2/0.441
3qwbNDPProbable quinone oxidoreductase1.6.5.50.441
4e2bFMNDehydrogenase/0.441
4fhf0TTSpore photoproduct lyase/0.441
4gk2L66Ephrin type-A receptor 32.7.10.10.441
4nbuNAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.441
5e8ySTUTGF-beta receptor type-22.7.11.300.441
1dhjMTXDihydrofolate reductase1.5.1.30.440
1draMTXDihydrofolate reductase1.5.1.30.440
1dz6CAMCamphor 5-monooxygenase1.14.15.10.440
1oyaFMNNADPH dehydrogenase 11.6.99.10.440
1rx1NAPDihydrofolate reductase1.5.1.30.440
1u2yGOXPancreatic alpha-amylase/0.440
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.440
2q3eNAIUDP-glucose 6-dehydrogenase1.1.1.220.440
2tpsTPSThiamine-phosphate synthase/0.440
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.440
3fwiCAMCamphor 5-monooxygenase1.14.15.10.440
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.440
3kb1ADPIron-sulfur cluster carrier protein/0.440
3umvFADDeoxyribodipyrimidine photo-lyase4.1.99.30.440
4dieC5PCytidylate kinase/0.440
4esoNAPPutative oxidoreductase/0.440
4fj2NAP17beta-hydroxysteroid dehydrogenase/0.440
4jicFMNGTN Reductase/0.440
4kl9NDPDihydrofolate reductase1.5.1.30.440
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.440
5im3DTPRibonucleoside-diphosphate reductase/0.440