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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
1ywgNADGlyceraldehyde-3-phosphate dehydrogenase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1ywgNADGlyceraldehyde-3-phosphate dehydrogenase/1.000
2b4rNADGlyceraldehyde-3-phosphate dehydrogenase/0.591
1u8fNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.588
3idsNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.569
4o63NADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.557
4z0hNADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic1.2.1.120.557
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.555
4o59NADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.553
3cifNADGlyceraldehyde-3-phosphate dehydrogenase/0.552
1rm5NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.549
4lsmNADGlyceraldehyde-3-phosphate dehydrogenase/0.543
3cpsNADGlyceraldehyde-3-phosphate dehydrogenase/0.542
4dbvNDPGlyceraldehyde-3-phosphate dehydrogenase/0.542
1vsvNADGlyceraldehyde-3-phosphate dehydrogenase/0.540
2d2iNAPGlyceraldehyde-3-phosphate dehydrogenase/0.537
3e5rNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.537
4p8rNADGlyceraldehyde-3-phosphate dehydrogenase/0.535
1nboNADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.534
1ihxSNDGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.533
4boyNADGlyceraldehyde-3-phosphate dehydrogenase/0.533
1ml3NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.532
1a7kNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.530
1gadNADGlyceraldehyde-3-phosphate dehydrogenase A/0.529
3gnqNADGlyceraldehyde-3-phosphate dehydrogenase/0.529
3ksdNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.529
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.528
3v1yNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.528
2dbvNDPGlyceraldehyde-3-phosphate dehydrogenase/0.527
1nptNADGlyceraldehyde-3-phosphate dehydrogenase/0.525
1rm4NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.520
2ep7NADGlyceraldehyde-3-phosphate dehydrogenase/0.520
1dbvNADGlyceraldehyde-3-phosphate dehydrogenase/0.519
1j0xNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.516
1vc2NADGlyceraldehyde-3-phosphate dehydrogenase/0.515
1szjNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.513
3dmtNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.513
1dc6NADGlyceraldehyde-3-phosphate dehydrogenase A/0.510
1znqNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.510
3lvfNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.507
1nq5NADGlyceraldehyde-3-phosphate dehydrogenase/0.506
3k2bNADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.506
4uymVOR14-alpha sterol demethylase Cyp51B/0.506
1qxsNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.504
3pymNADGlyceraldehyde-3-phosphate dehydrogenase 31.2.1.120.504
5c7oNADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific1.2.1.120.500
3b20NADGlyceraldehyde-3-phosphate dehydrogenase/0.498
1jn0NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.495
3zcxNADGlyceraldehyde-3-phosphate dehydrogenase/0.494
1rm3NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.488
2pkrNDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic1.2.1.130.485
3l4sNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.485
1gpdNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.484
2cy0NAPShikimate dehydrogenase (NADP(+))/0.484
1ihyAPRGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.482
1g1aNADdTDP-glucose 4,6-dehydratase/0.480
4ipw1G7Mycocyclosin synthase1.14.21.90.479
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.478
3l0dNADGlyceraldehyde-3-phosphate dehydrogenase/0.478
4g090VDHistidinol dehydrogenase/0.478
2i3gNAPN-acetyl-gamma-glutamyl-phosphate reductase1.2.1.380.477
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.477
4dreNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.476
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.475
5eioNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.475
2jcxNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.474
3g5hYTTMycocyclosin synthase1.14.21.90.473
1gcoNADGlucose 1-dehydrogenase1.1.1.470.472
2gjlFMNNitronate monooxygenase1.13.12.160.472
3c1y2BADNA integrity scanning protein DisA/0.472
3gfbNADL-threonine 3-dehydrogenase/0.472
3r9uFADThioredoxin reductase/0.472
1xddAAYIntegrin alpha-L/0.471
2cvuCDPRibonucleoside-diphosphate reductase large chain 11.17.4.10.469
4g3jVNTLanosterol 14-alpha-demethylase/0.469
1ia1NDPDihydrofolate reductase1.5.1.30.468
3gw9VNILanosterol 14-alpha-demethylase/0.468
3triNAPPyrroline-5-carboxylate reductase/0.468
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.468
1o9bNAIQuinate/shikimate dehydrogenase/0.467
2rkvZBATrichothecene 3-O-acetyltransferase/0.467
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.467
4e5yNDPGDP-L-fucose synthase1.1.1.2710.467
4g7gVFVLanosterol 14-alpha-demethylase/0.467
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.467
5hs1VORLanosterol 14-alpha demethylase/0.467
1hfqMOTDihydrofolate reductase1.5.1.30.466
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.466
1m78NDPDihydrofolate reductase1.5.1.30.465
1tl7FOKAdenylate cyclase type 2/0.465
1tl7FOKAdenylate cyclase type 5/0.465
1kkq471Peroxisome proliferator-activated receptor alpha/0.464
1w6hTITPlasmepsin-23.4.23.390.464
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.464
1jioDEB6-deoxyerythronolide B hydroxylase/0.463
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.463
3frqERYErythromycin resistance repressor protein/0.463
3o0oGDPVitamin B12-dependent ribonucleotide reductase/0.463
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.462
1u3dFADCryptochrome-1/0.462
1xe55FEPlasmepsin-23.4.23.390.462
2ntvP1HEnoyl-[acyl-carrier-protein] reductase [NADH]/0.462
4bfxZVXPantothenate kinase2.7.1.330.462
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.462
1u3cFADCryptochrome-1/0.461
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.461
3umvFADDeoxyribodipyrimidine photo-lyase4.1.99.30.461
4i8vBHFCytochrome P450 1A11.14.14.10.461
1nqaNADGlyceraldehyde-3-phosphate dehydrogenase/0.460
4ips1G4Mycocyclosin synthase1.14.21.90.459
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.458
3ibqATPPyridoxal kinase/0.458
3ieuGDPGTPase Era/0.458
3tjzGNPADP-ribosylation factor 1/0.458
4a6cQG9Gag-Pol polyprotein3.4.23.160.458
4nmdFDABifunctional protein PutA/0.458
1cjkFOKAdenylate cyclase type 2/0.457
1cjkFOKAdenylate cyclase type 5/0.457
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.457
2vtbFADCryptochrome DASH, chloroplastic/mitochondrial/0.457
3bheBZNGag-Pol polyprotein3.4.23.160.457
3toxNAPPutative oxidoreductase/0.457
4q72FADBifunctional protein PutA/0.457
2cvwGDPRibonucleoside-diphosphate reductase large chain 11.17.4.10.456
3el01UNGag-Pol polyprotein3.4.23.160.456
4l4fCAMCamphor 5-monooxygenase1.14.15.10.456
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.455
1pjcNADAlanine dehydrogenase/0.455
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.455
3il1B5DGlutamate receptor 2/0.455
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.455
4enhFVXCholesterol 24-hydroxylase/0.455
1c1dNAIPhenylalanine dehydrogenase/0.454
1h50FMNPentaerythritol tetranitrate reductase/0.454
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.454
1kh3ANPArgininosuccinate synthase/0.454
1omoNADAlanine dehydrogenase/0.454
1rx1NAPDihydrofolate reductase1.5.1.30.454
3b6zCO7Enoyl reductase LovC10.454
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.454
4dpuAGSMevalonate diphosphate decarboxylase/0.454
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.454
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
1o76CAMCamphor 5-monooxygenase1.14.15.10.453
2ejzSAHDiphthine synthase/0.453
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.453
3mdmFJZCholesterol 24-hydroxylase/0.453
3p62FMNPentaerythritol tetranitrate reductase/0.453
4a6bQG8Gag-Pol polyprotein3.4.23.160.453
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.453
4gk3L87Ephrin type-A receptor 32.7.10.10.453
5e8wSTUTGF-beta receptor type-12.7.11.300.453
5f8eSAHPossible transcriptional regulatory protein/0.453
1bw9NADPhenylalanine dehydrogenase/0.452
1dhrNADDihydropteridine reductase1.5.1.340.452
2bxmIMNSerum albumin/0.452
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.452
4q71FADBifunctional protein PutA/0.452
4q73FADBifunctional protein PutA/0.452
4tuvCPZCytochrome P450 1191.140.452
1tehNADAlcohol dehydrogenase class-31.1.1.10.451
1vzdCB3Thymidylate synthase/0.451
3qlrNDPDihydrofolate reductase1.5.1.30.451
3uylTYDProbable NDP-rhamnosyltransferase/0.451
4hxyNDPPlm1/0.451
4m6jNDPDihydrofolate reductase1.5.1.30.451
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.451
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.450
1g6kNADGlucose 1-dehydrogenase1.1.1.470.450
1jolFFODihydrofolate reductase1.5.1.30.450
1rfuADPPyridoxal kinase2.7.1.350.450
1xe65FPPlasmepsin-23.4.23.390.450
1zidZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.450
2zjaACPATP-dependent DNA helicase Hel308/0.450
3cisATPUniversal stress protein Rv2623/0.450
3qlsNDPDihydrofolate reductase1.5.1.30.450
3u4cNDPNADPH-dependent reductase BacG/0.450
5d3qGDPDynamin-13.6.5.50.450
1bwsNDPGDP-L-fucose synthase/0.449
1fmlRTLRetinol dehydratase/0.449
2rhrEMOPutative ketoacyl reductase1.3.10.449
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.449
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.449
4i6gFADCryptochrome-2/0.449
1culFOKAdenylate cyclase type 2/0.448
1culFOKAdenylate cyclase type 5/0.448
2qboCAMCamphor 5-monooxygenase1.14.15.10.448
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
5a3bAPRSIR2 family protein/0.448
5c8wPCGcGMP-dependent protein kinase 22.7.11.120.448
1nzfUPGDNA beta-glucosyltransferase/0.447
1rfvADPPyridoxal kinase2.7.1.350.447
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
3bc3OPTCathepsin L13.4.22.150.447
3gwfFADCyclohexanone monooxygenase/0.447
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.447
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.447
4bfvZVVPantothenate kinase2.7.1.330.447
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.447
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.447
4y0kNAPAntE/0.447
1cs4FOKAdenylate cyclase type 2/0.446
1cs4FOKAdenylate cyclase type 5/0.446
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1e3eNAIAlcohol dehydrogenase 41.1.1.10.446
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.446
2qw034Z4-chlorobenzoyl CoA ligase/0.446
3ijoB4DGlutamate receptor 2/0.446
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
3tbaADPRibonucleoside-diphosphate reductase large chain 11.17.4.10.446
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.446
4m83ERYOleandomycin glycosyltransferase2.4.10.446
4u7wNDPMxaA/0.446
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.446
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.445
1mjbACOHistone acetyltransferase ESA1/0.445
1t2cNAIL-lactate dehydrogenase1.1.1.270.445
2qbuSAHPrecorrin-2 methyltransferase/0.445
3f03FMNPentaerythritol tetranitrate reductase/0.445
3gobHXXDdmC/0.445
3lqfNADGalactitol dehydrogenase/0.445
3smkCW714-3-3 protein sigma/0.445
3u9eCOALmo1369 protein/0.445
4cdmFO1Deoxyribodipyrimidine photolyase/0.445
4ejmNAPPutative zinc-binding dehydrogenase/0.445
4jyzATPGlutamine--tRNA ligase6.1.1.180.445
4ktl1CQCytochrome P450/0.445
4oqyNDP(S)-imine reductase/0.445
4r81FMNPredicted NADH dehydrogenase/0.445
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.445
1g4tFTPThiamine-phosphate synthase/0.444
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.444
2e07SAHDiphthine synthase/0.444
2ij7TPFMycocyclosin synthase1.14.21.90.444
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.444
3l63CAMCamphor 5-monooxygenase1.14.15.10.444
3oeyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
3otwCOAPhosphopantetheine adenylyltransferase/0.444
3s8cCDPRibonucleoside-diphosphate reductase large chain 11.17.4.10.444
3u8w09JMitogen-activated protein kinase 14/0.444
3udn09BBeta-secretase 13.4.23.460.444
3wbbNAPMeso-diaminopimelate D-dehydrogenase/0.444
3zuyTCHTransporter/0.444
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
4i8zG08Gag-Pol polyprotein3.4.23.160.444
4iwo1H4Serine/threonine-protein kinase TBK12.7.11.10.444
4l6gCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.444
4qecNAPElxO/0.444
4tqgNDPPutative dTDP-d-glucose 4 6-dehydratase/0.444
5a9sNAPPutative dehydrogenase/0.444
1ezvUQ6Cytochrome b/0.443
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
2he5NDPAldo-keto reductase family 1 member C211.1.10.443
2o4cNADErythronate-4-phosphate dehydrogenase/0.443
2vn0TDZCytochrome P450 2C8/0.443
2vynNADGlyceraldehyde-3-phosphate dehydrogenase A/0.443
3cd3STUTyrosine-protein kinase Fes/Fps2.7.10.20.443
3cppCAMCamphor 5-monooxygenase1.14.15.10.443
3f8rNAPNADH oxidase/thioredoxin reductase/0.443
3oewNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
3wb2YGPUncharacterized protein MJ0488/0.443
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
4i1iNADMalate dehydrogenase/0.443
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
4v2gITCTetracycline repressor protein class D/0.443
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.443
1adfTADAlcohol dehydrogenase E chain1.1.1.10.442
1geeNADGlucose 1-dehydrogenase1.1.1.470.442
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.442
1h51FMNPentaerythritol tetranitrate reductase/0.442
2c29NAPDihydroflavonol 4-reductase/0.442
2d8aNADL-threonine 3-dehydrogenase/0.442
2i4qUA4Renin3.4.23.150.442
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.442
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.442
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.442
3vyeVYERenin3.4.23.150.442
5irnADPNucleotide binding oligomerization domain containing 2/0.442
1cjvFOKAdenylate cyclase type 2/0.441
1cjvFOKAdenylate cyclase type 5/0.441
1k6cMK1Gag-Pol polyprotein3.4.23.160.441
1nvtNAPShikimate dehydrogenase (NADP(+))/0.441
1toiHCIAspartate aminotransferase2.6.1.10.441
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.441
2g1o2IGRenin3.4.23.150.441
2qo9ANPEphrin type-A receptor 32.7.10.10.441
3a4vNADNDP-sugar epimerase/0.441
3atzFMNProstaglandin F2a synthase/0.441
3k4nFADPyranose 2-oxidase/0.441
3vvpBNUUncharacterized protein/0.441
4lcg1WMUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.441
4njsG08Protease/0.441
4qmzB49Serine/threonine-protein kinase 242.7.11.10.441
4rrvATP3-phosphoinositide-dependent protein kinase 12.7.11.10.441
1dr2TAPDihydrofolate reductase1.5.1.30.440
1npvL27Gag-Pol polyprotein3.4.23.160.440
2aqhNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
2ejvNADL-threonine 3-dehydrogenase/0.440
2iyfERYOleandomycin glycosyltransferase2.4.10.440
2yylFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.440
3q3cNADNAD-dependent L-serine dehydrogenase/0.440
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.440
3zs7ATPPyridoxine/pyridoxal/pyridoxamine kinase/0.440
4dfg0JVGag-Pol polyprotein3.4.23.160.440
4lopSB4Mitogen-activated protein kinase 14/0.440
4qmySTUSerine/threonine-protein kinase 242.7.11.10.440
4xymCOAAcyl-CoA synthetase (NDP forming)/0.440