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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
2egbSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2egbSAHDiphthine synthase/1.000
2e08SAHDiphthine synthase/0.858
2egsSAHDiphthine synthase/0.852
2p2xSAHDiphthine synthase/0.760
2e7rSAHDiphthine synthase/0.754
2p5fSAHDiphthine synthase/0.753
2p6dSAHDiphthine synthase/0.748
2p6iSAHDiphthine synthase/0.746
2ejkSAHDiphthine synthase/0.744
2eleSAHDiphthine synthase/0.744
2ekaSAHDiphthine synthase/0.734
2eglSAHDiphthine synthase/0.732
2pcgSAHDiphthine synthase/0.732
2dxvSAHDiphthine synthase/0.728
2ehlSAHDiphthine synthase/0.727
2owuSAHDiphthine synthase/0.726
2dxwSAHDiphthine synthase/0.725
2p5cSAHDiphthine synthase/0.713
2emrSAHDiphthine synthase/0.708
2e8hSAHDiphthine synthase/0.703
2eniSAHDiphthine synthase/0.703
2owvSAHDiphthine synthase/0.703
2p6kSAHDiphthine synthase/0.701
2dxxSAHDiphthine synthase/0.700
2pchSAHDiphthine synthase/0.697
2dv7SAHDiphthine synthase/0.694
2ed5SAHDiphthine synthase/0.694
2dshSAHDiphthine synthase/0.693
2pcmSAHDiphthine synthase/0.691
2eh5SAHDiphthine synthase/0.689
2pckSAHDiphthine synthase/0.678
2owkSAHDiphthine synthase/0.675
2eeqSAHDiphthine synthase/0.672
2ek7SAHDiphthine synthase/0.672
2dekSAHDiphthine synthase/0.670
2ejjSAHDiphthine synthase/0.670
2pb5SAHDiphthine synthase/0.670
1vceSAHDiphthine synthase/0.668
2el0SAHDiphthine synthase/0.667
2hr8SAHDiphthine synthase/0.666
2ek3SAHDiphthine synthase/0.653
2huqSAHDiphthine synthase/0.653
2e16SAHDiphthine synthase/0.651
2pb4SAHDiphthine synthase/0.651
2pciSAHDiphthine synthase/0.651
2dsiSAHDiphthine synthase/0.650
2e8sSAHDiphthine synthase/0.648
2emuSAHDiphthine synthase/0.648
2e15SAHDiphthine synthase/0.644
2en5SAHDiphthine synthase/0.642
2e07SAHDiphthine synthase/0.640
2dv3SAHDiphthine synthase/0.637
2eh4SAHDiphthine synthase/0.637
2owgSAHDiphthine synthase/0.630
2e8qSAHDiphthine synthase/0.628
2pcaSAHDiphthine synthase/0.627
2p9dSAHDiphthine synthase/0.622
2dv5SAHDiphthine synthase/0.618
2dv4SAHDiphthine synthase/0.614
2eh2SAHDiphthine synthase/0.610
2eldSAHDiphthine synthase/0.606
2hutSAHDiphthine synthase/0.605
2e8rSAHDiphthine synthase/0.602
2ed3SAHDiphthine synthase/0.602
2el3SAHDiphthine synthase/0.602
1wngSAHDiphthine synthase/0.592
2ek4SAHDiphthine synthase/0.592
2dsgSAHDiphthine synthase/0.591
2z6rSAHDiphthine synthase/0.590
2e17SAHDiphthine synthase/0.589
2huvSAHDiphthine synthase/0.588
2huxSAHDiphthine synthase/0.587
2p6lSAHDiphthine synthase/0.581
2owfSAHDiphthine synthase/0.573
2ejzSAHDiphthine synthase/0.572
2e4nSAHDiphthine synthase/0.559
2pb6SAHDiphthine synthase/0.539
2ek2SAHDiphthine synthase/0.526
1lbcCYZGlutamate receptor 2/0.491
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.490
2xhd7T9Glutamate receptor 2/0.483
2ifaFMNUncharacterized protein/0.476
4a8v2ANMajor pollen allergen Bet v 1-J/0.476
1xe55FEPlasmepsin-23.4.23.390.475
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.474
4wriOKAOkadaic acid binding protein 2-alpha/0.474
1tqf32PBeta-secretase 13.4.23.460.473
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.473
1rneC60Renin3.4.23.150.472
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.471
3bc3OPTCathepsin L13.4.22.150.471
3ijoB4DGlutamate receptor 2/0.470
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.470
4nbwNADShort-chain dehydrogenase/reductase SDR/0.470
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.468
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.468
4g3jVNTLanosterol 14-alpha-demethylase/0.468
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.468
1dirNADDihydropteridine reductase1.5.1.340.467
1zeoC01Peroxisome proliferator-activated receptor gamma/0.465
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.465
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.464
2zvcSAHPrecorrin-3 C17-methyltransferase/0.463
4i1iNADMalate dehydrogenase/0.463
1rfuADPPyridoxal kinase2.7.1.350.462
1vp6CMPCyclic nucleotide-gated potassium channel mll3241/0.462
2rcyNAPPyrroline-5-carboxylate reductase/0.462
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
2p5uNADUDP-glucose 4-epimerase/0.461
3in6FMNUncharacterized protein/0.461
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.461
1kkq471Peroxisome proliferator-activated receptor alpha/0.460
1xddAAYIntegrin alpha-L/0.460
4dpuAGSMevalonate diphosphate decarboxylase/0.460
2q5g1FAPeroxisome proliferator-activated receptor delta/0.459
1ma0NADAlcohol dehydrogenase class-31.1.1.10.458
4bfzZVZPantothenate kinase2.7.1.330.458
4g7gVFVLanosterol 14-alpha-demethylase/0.458
2g1s4IGRenin3.4.23.150.457
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.456
1udaUFGUDP-glucose 4-epimerase5.1.3.20.456
2gjlFMNNitronate monooxygenase1.13.12.160.456
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.456
2npaMMBPeroxisome proliferator-activated receptor alpha/0.456
3kb1ADPIron-sulfur cluster carrier protein/0.456
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.456
1ptjNAPNAD(P) transhydrogenase subunit beta1.6.1.20.455
2rlcCHDCholoylglycine hydrolase3.5.1.240.455
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.455
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.454
1x1aSAMC-20 methyltransferase/0.454
2ovhAS0Progesterone receptor/0.454
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.454
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.454
1g1aNADdTDP-glucose 4,6-dehydratase/0.453
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.453
3vqsJT1Genome polyprotein/0.453
4ji91M3Tyrosine-protein kinase JAK2/0.453
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.453
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.453
5irnADPNucleotide binding oligomerization domain containing 2/0.453
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.452
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.452
3f3sNADLambda-crystallin homolog/0.452
3vt8YI3Vitamin D3 receptor/0.452
4egbNADdTDP-glucose 4,6-dehydratase/0.452
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.452
5fm7ADPRuvB-like helicase/0.452
1eh4IC1Casein kinase I homolog 12.7.11.10.451
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
2qbuSAHPrecorrin-2 methyltransferase/0.451
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.451
1o97FADElectron transfer flavoprotein subunit alpha/0.450
2ahrNAPPyrroline-5-carboxylate reductase/0.450
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.450
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.450
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
5dp2NAPCurF/0.450
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.450
1bmfANPATP synthase subunit alpha, mitochondrial/0.449
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.449
1h8hATPATP synthase subunit alpha, mitochondrial/0.449
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.449
1xl5190Gag-Pol polyprotein3.4.23.160.449
3gw9VNILanosterol 14-alpha-demethylase/0.449
3gwfNAPCyclohexanone monooxygenase/0.449
3ut5LOCTubulin beta chain/0.449
1t2cNAIL-lactate dehydrogenase1.1.1.270.448
1w6hTITPlasmepsin-23.4.23.390.448
1yb5NAPQuinone oxidoreductase1.6.5.50.448
2gjnFMNNitronate monooxygenase1.13.12.160.448
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
3to6LYS_CMCHistone acetyltransferase ESA1/0.448
4dx9SER_ALA_VAL_THRIntegrin beta-1/0.448
4dx9SER_ALA_VAL_THRIntegrin beta-1-binding protein 1/0.448
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.448
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.448
1phgMYTCamphor 5-monooxygenase1.14.15.10.447
2a94AP0L-lactate dehydrogenase1.1.1.270.447
2hrcCHDFerrochelatase, mitochondrial4.99.1.10.447
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.447
4eudCOASuccinyl-CoA:acetate CoA-transferase/0.447
4i8zG08Gag-Pol polyprotein3.4.23.160.447
1g63FMNEpidermin decarboxylase4.1.10.446
1x1cSAHC-20 methyltransferase/0.446
2am22LGUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.446
2givACOHistone acetyltransferase KAT8/0.446
3zh8C58Protein kinase C iota type2.7.11.130.446
4djy0KRBeta-secretase 13.4.23.460.446
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.446
4qecNAPElxO/0.446
1f8fNADBenzyl alcohol dehydrogenase/0.445
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.445
1obbNADAlpha-glucosidase3.2.1.200.445
1vikBAYGag-Pol polyprotein/0.445
1xe65FPPlasmepsin-23.4.23.390.445
2fgkATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.445
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.445
2uxpCLMHTH-type transcriptional regulator TtgR/0.445
2w06FRVCyclin-dependent kinase 22.7.11.220.445
3ajrNADNDP-sugar epimerase/0.445
3ig6438Urokinase-type plasminogen activator3.4.21.730.445
3sdi3SDProteasome subunit beta type-53.4.25.10.445
3sdi3SDProteasome subunit beta type-63.4.25.10.445
4a862ANMajor pollen allergen Bet v 1-A/0.445
1gvhFADFlavohemoprotein/0.444
1m8jNADNicotinamide-nucleotide adenylyltransferase2.7.7.10.444
1rfvADPPyridoxal kinase2.7.1.350.444
1v9aSAHUncharacterized protein/0.444
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.444
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.444
3c1y2BADNA integrity scanning protein DisA/0.444
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.444
1f8wFADNADH peroxidase1.11.1.10.443
1pjcNADAlanine dehydrogenase/0.443
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.443
1x1dSAHC-20 methyltransferase/0.443
2a87FADThioredoxin reductase1.8.1.90.443
2b53D23Cyclin-dependent kinase 22.7.11.220.443
2c3lIDZSerine/threonine-protein kinase Chk12.7.11.10.443
2ep7NADGlyceraldehyde-3-phosphate dehydrogenase/0.443
2gv8NDPThiol-specific monooxygenase1.14.130.443
2gz7D3FOrf1a polyprotein/0.443
2pj4414Carboxypeptidase B/0.443
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.443
3adaNADSubunit alpha of sarocosine oxidase/0.443
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4b1bFADThioredoxin reductase1.8.1.90.443
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.443
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.443
5c1mCLRMu-type opioid receptor/0.443
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1nyxDRFPeroxisome proliferator-activated receptor gamma/0.442
1q8wM77cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
2fznFADBifunctional protein PutA1.5.5.20.442
2rhgIGPTryptophan synthase alpha chain/0.442
2uzwSS4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
2yylFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.442
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3pndFADFAD:protein FMN transferase/0.442
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.442
3wb2YGPUncharacterized protein MJ0488/0.442
4yryFADGlutamate synthase, beta subunit/0.442
1beuIPLTryptophan synthase alpha chain/0.441
1ja0FMNNADPH--cytochrome P450 reductase/0.441
1o0sNAINAD-dependent malic enzyme, mitochondrial1.1.1.380.441
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2fy4COACholine O-acetyltransferase2.3.1.60.441
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.441
3orfNADDihydropteridine reductase1.5.1.340.441
3sz0FADSulfide-quinone reductase/0.441
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.441
3tneRITCandidapepsin-13.4.23.240.441
4frkDWDBeta-secretase 13.4.23.460.441
4h3j10WBeta-secretase 13.4.23.460.441
4m4922YL-lactate dehydrogenase A chain1.1.1.270.441
1f20FADNitric oxide synthase, brain1.14.13.390.440
1qiqACCIsopenicillin N synthase1.21.3.10.440
1qorNDPQuinone oxidoreductase 1/0.440
1tj0FADBifunctional protein PutA1.5.5.20.440
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.440
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.440
3b70NAPEnoyl reductase LovC10.440
3h06VBPGlutamate receptor 2/0.440
3nutSAHPrecorrin-3 methylase/0.440
3so9017Pol protein/0.440
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4z4pSAHHistone-lysine N-methyltransferase 2D2.1.1.430.440
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.440