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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
2dxwSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2dxwSAHDiphthine synthase/1.000
2dxvSAHDiphthine synthase/0.920
2e8sSAHDiphthine synthase/0.894
2emrSAHDiphthine synthase/0.880
2pcmSAHDiphthine synthase/0.850
2dv7SAHDiphthine synthase/0.845
2eniSAHDiphthine synthase/0.831
2eh5SAHDiphthine synthase/0.827
2el0SAHDiphthine synthase/0.825
2ed5SAHDiphthine synthase/0.824
2e8qSAHDiphthine synthase/0.823
2ejkSAHDiphthine synthase/0.822
2ek7SAHDiphthine synthase/0.822
2p6kSAHDiphthine synthase/0.822
2emuSAHDiphthine synthase/0.809
2eglSAHDiphthine synthase/0.803
2pb4SAHDiphthine synthase/0.798
2dsgSAHDiphthine synthase/0.792
2ehlSAHDiphthine synthase/0.791
2egsSAHDiphthine synthase/0.788
2p6dSAHDiphthine synthase/0.784
2en5SAHDiphthine synthase/0.779
2dv4SAHDiphthine synthase/0.773
2p2xSAHDiphthine synthase/0.769
2ekaSAHDiphthine synthase/0.767
2p5cSAHDiphthine synthase/0.746
2huxSAHDiphthine synthase/0.741
1wngSAHDiphthine synthase/0.734
2e7rSAHDiphthine synthase/0.729
2egbSAHDiphthine synthase/0.724
2p5fSAHDiphthine synthase/0.713
2e16SAHDiphthine synthase/0.707
2owvSAHDiphthine synthase/0.706
2owkSAHDiphthine synthase/0.702
2pchSAHDiphthine synthase/0.700
2pcaSAHDiphthine synthase/0.699
2pb6SAHDiphthine synthase/0.698
2eleSAHDiphthine synthase/0.697
2dxxSAHDiphthine synthase/0.696
2pcgSAHDiphthine synthase/0.693
2dv3SAHDiphthine synthase/0.692
2dsiSAHDiphthine synthase/0.691
2eh2SAHDiphthine synthase/0.687
2e08SAHDiphthine synthase/0.683
1vceSAHDiphthine synthase/0.675
2pb5SAHDiphthine synthase/0.669
2p6iSAHDiphthine synthase/0.664
2e8hSAHDiphthine synthase/0.660
2hutSAHDiphthine synthase/0.660
2z6rSAHDiphthine synthase/0.658
2eh4SAHDiphthine synthase/0.657
2ek2SAHDiphthine synthase/0.654
2hr8SAHDiphthine synthase/0.654
2owgSAHDiphthine synthase/0.652
2huvSAHDiphthine synthase/0.651
2eeqSAHDiphthine synthase/0.646
2owuSAHDiphthine synthase/0.644
2e4nSAHDiphthine synthase/0.643
2dekSAHDiphthine synthase/0.642
2pckSAHDiphthine synthase/0.642
2ejjSAHDiphthine synthase/0.641
2p9dSAHDiphthine synthase/0.640
2dv5SAHDiphthine synthase/0.635
2pciSAHDiphthine synthase/0.632
2ek4SAHDiphthine synthase/0.630
2eldSAHDiphthine synthase/0.622
2e07SAHDiphthine synthase/0.619
2e17SAHDiphthine synthase/0.619
2ek3SAHDiphthine synthase/0.618
2e8rSAHDiphthine synthase/0.615
2el3SAHDiphthine synthase/0.605
2p6lSAHDiphthine synthase/0.596
2huqSAHDiphthine synthase/0.588
2owfSAHDiphthine synthase/0.571
2dshSAHDiphthine synthase/0.556
2ed3SAHDiphthine synthase/0.555
2e15SAHDiphthine synthase/0.540
2ejzSAHDiphthine synthase/0.538
1xe55FEPlasmepsin-23.4.23.390.507
2y3sTIRTamL/0.505
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.491
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.485
1f8fNADBenzyl alcohol dehydrogenase/0.483
1g63FMNEpidermin decarboxylase4.1.10.483
1zeoC01Peroxisome proliferator-activated receptor gamma/0.483
1lbcCYZGlutamate receptor 2/0.480
4g3jVNTLanosterol 14-alpha-demethylase/0.478
3b70NAPEnoyl reductase LovC10.477
1xe65FPPlasmepsin-23.4.23.390.476
3ig6438Urokinase-type plasminogen activator3.4.21.730.476
2xhd7T9Glutamate receptor 2/0.474
2pswCOAN-alpha-acetyltransferase 50/0.473
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.472
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.472
4h3f10OBeta-secretase 13.4.23.460.472
4g7gVFVLanosterol 14-alpha-demethylase/0.471
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.470
1tqf32PBeta-secretase 13.4.23.460.470
3gw9VNILanosterol 14-alpha-demethylase/0.470
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.470
1kp3ATPArgininosuccinate synthase6.3.4.50.469
2a94AP0L-lactate dehydrogenase1.1.1.270.469
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.469
2dftADPShikimate kinase2.7.1.710.467
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.467
2he5NDPAldo-keto reductase family 1 member C211.1.10.466
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.465
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.465
4r21STRCytochrome P450 family 17 polypeptide 2/0.465
3a3gDLZLumazine protein/0.464
4m83ERYOleandomycin glycosyltransferase2.4.10.464
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.464
1j3kNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.463
1w6hTITPlasmepsin-23.4.23.390.463
2q5g1FAPeroxisome proliferator-activated receptor delta/0.463
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.462
1x1aSAMC-20 methyltransferase/0.462
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.462
1bwsNDPGDP-L-fucose synthase/0.461
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.461
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.461
1dirNADDihydropteridine reductase1.5.1.340.460
2znnS44Peroxisome proliferator-activated receptor alpha/0.460
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
4nbwNADShort-chain dehydrogenase/reductase SDR/0.460
1nzdUPGDNA beta-glucosyltransferase/0.459
2g1s4IGRenin3.4.23.150.459
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.459
4egbNADdTDP-glucose 4,6-dehydratase/0.459
1h8hATPATP synthase subunit alpha, mitochondrial/0.458
1h8hATPATP synthase subunit beta, mitochondrial3.6.3.140.458
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.458
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.458
4b78KGGBeta-secretase 13.4.23.460.458
4bfzZVZPantothenate kinase2.7.1.330.458
4wriOKAOkadaic acid binding protein 2-alpha/0.458
4xr9NADCalS8/0.458
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.458
1e1qANPATP synthase subunit alpha, mitochondrial/0.457
1e1qANPATP synthase subunit beta, mitochondrial3.6.3.140.457
2b8l5HABeta-secretase 13.4.23.460.457
2ifaFMNUncharacterized protein/0.457
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.457
4a862ANMajor pollen allergen Bet v 1-A/0.457
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
1mp0NADAlcohol dehydrogenase class-31.1.1.10.456
1x1dSAHC-20 methyltransferase/0.456
2oapANPType II secretion system protein (GspE-2)/0.456
2q7vFADThioredoxin reductase/0.456
2qbuSAHPrecorrin-2 methyltransferase/0.456
3ijoB4DGlutamate receptor 2/0.456
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.456
1ma0NADAlcohol dehydrogenase class-31.1.1.10.455
1xddAAYIntegrin alpha-L/0.455
2p5uNADUDP-glucose 4-epimerase/0.455
2pj4414Carboxypeptidase B/0.455
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.455
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.455
3vqsJT1Genome polyprotein/0.455
1mjbACOHistone acetyltransferase ESA1/0.454
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.454
2zvcSAHPrecorrin-3 C17-methyltransferase/0.454
3slkNDPPolyketide synthase extender module 2/0.454
4ejmNAPPutative zinc-binding dehydrogenase/0.454
5hwsNAP2-dehydropantoate 2-reductase/0.454
1g1aNADdTDP-glucose 4,6-dehydratase/0.453
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.453
2bjfDXCCholoylglycine hydrolase3.5.1.240.453
3tneRITCandidapepsin-13.4.23.240.453
4i8zG08Gag-Pol polyprotein3.4.23.160.453
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
1t2cNAIL-lactate dehydrogenase1.1.1.270.452
1xs7MMIBeta-secretase 13.4.23.460.452
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.452
4b7754MBeta-secretase 13.4.23.460.452
4ipw1G7Mycocyclosin synthase1.14.21.90.452
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.452
1ep3FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.451
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.451
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.451
2g1r3IGRenin3.4.23.150.451
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.451
2rlcCHDCholoylglycine hydrolase3.5.1.240.451
2znq401Peroxisome proliferator-activated receptor delta/0.451
4h3j10WBeta-secretase 13.4.23.460.451
4irnFADAnaB/0.451
4kb9G79Protease/0.451
5dp2NAPCurF/0.451
5irnADPNucleotide binding oligomerization domain containing 2/0.451
1bmfANPATP synthase subunit alpha, mitochondrial/0.450
1bmfANPATP synthase subunit beta, mitochondrial3.6.3.140.450
1u3dFADCryptochrome-1/0.450
1v9aSAHUncharacterized protein/0.450
1x1cSAHC-20 methyltransferase/0.450
2gjlFMNNitronate monooxygenase1.13.12.160.450
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.450
3wb2YGPUncharacterized protein MJ0488/0.450
4emtC2EStimulator of interferon genes protein/0.450
4i1iNADMalate dehydrogenase/0.450
1f8wFADNADH peroxidase1.11.1.10.449
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1y4lSVRBasic phospholipase A2 homolog 2/0.449
2is0I03Beta-secretase 13.4.23.460.449
2x06NADL-sulfolactate dehydrogenase/0.449
2zjmF1MBeta-secretase 13.4.23.460.449
4a8v2ANMajor pollen allergen Bet v 1-J/0.449
4dbzNDPPutative ketoacyl reductase1.3.10.449
4wudANPDNA gyrase subunit B/0.449
4xguADPPutative pachytene checkpoint protein 2/0.449
2fznFADBifunctional protein PutA1.5.5.20.448
2rcyNAPPyrroline-5-carboxylate reductase/0.448
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4bfxZVXPantothenate kinase2.7.1.330.448
4lutDCSAlanine racemase/0.448
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
1pjcNADAlanine dehydrogenase/0.447
2a5kAZPReplicase polyprotein 1ab3.4.220.447
2gv8NDPThiol-specific monooxygenase1.14.130.447
4ambDUDPutative glycosyl transferase/0.447
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.447
4bf2STUMitogen-activated protein kinase kinase kinase 52.7.11.250.447
4q71FADBifunctional protein PutA/0.447
5af7FADAcyl-CoA dehydrogenase/0.447
2g226IGRenin3.4.23.150.446
3orfNADDihydropteridine reductase1.5.1.340.446
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.446
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.446
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.446
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.446
1x1bSAHC-20 methyltransferase/0.445
2b53D23Cyclin-dependent kinase 22.7.11.220.445
2cftPLPPyridoxal phosphate phosphatase/0.445
2g1o2IGRenin3.4.23.150.445
2q4bNAPUncharacterized protein At5g02240/0.445
2znpK55Peroxisome proliferator-activated receptor delta/0.445
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3ixp834Ecdysone receptor/0.445
3q43D66M1 family aminopeptidase3.4.110.445
4rquNADAlcohol dehydrogenase class-P/0.445
1fm4DXCMajor pollen allergen Bet v 1-L/0.444
1me6IVSPlasmepsin-23.4.23.390.444
1mjaCOAHistone acetyltransferase ESA1/0.444
2g1y5IGRenin3.4.23.150.444
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
2vwqNAPGlucose 1-dehydrogenase/0.444
2wo7ASVIsopenicillin N synthase1.21.3.10.444
2zvbSAHPrecorrin-3 C17-methyltransferase/0.444
3jziJZLBiotin carboxylase6.3.4.140.444
3s1dZIRCytokinin dehydrogenase 11.5.99.120.444
4acxS8ZBeta-secretase 13.4.23.460.444
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
4djy0KRBeta-secretase 13.4.23.460.444
1bim0QBRenin3.4.23.150.443
1jedADPSulfate adenylyltransferase/0.443
1tj0FADBifunctional protein PutA1.5.5.20.443
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
2xx91NFGlutamate receptor 2/0.443
3mdmFJZCholesterol 24-hydroxylase/0.443
3ut5LOCTubulin beta chain/0.443
4f5yC2EStimulator of interferon genes protein/0.443
1k7fIAVTryptophan synthase alpha chain/0.442
1vikBAYGag-Pol polyprotein/0.442
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.442
2iyfERYOleandomycin glycosyltransferase2.4.10.442
3bc3OPTCathepsin L13.4.22.150.442
3zuyTCHTransporter/0.442
4dpy2P0Mevalonate diphosphate decarboxylase/0.442
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.442
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.442
4px9ADPATP-dependent RNA helicase DDX3X3.6.4.130.442
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.442
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.442
1fy7COAHistone acetyltransferase ESA1/0.441
1nhhANPDNA mismatch repair protein MutL/0.441
1tehNADAlcohol dehydrogenase class-31.1.1.10.441
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.441
2irzI02Beta-secretase 13.4.23.460.441
2op9WR1Orf1ab polyprotein/0.441
2ph6712Beta-secretase 13.4.23.460.441
2uxoTACHTH-type transcriptional regulator TtgR/0.441
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.441
4ejvLCLTranscriptional regulator TcaR/0.441
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.441
4tuvCPZCytochrome P450 1191.140.441
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1a72PADAlcohol dehydrogenase E chain1.1.1.10.440
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1xl5190Gag-Pol polyprotein3.4.23.160.440
2rh9IGPTryptophan synthase alpha chain/0.440
2wedPP6Penicillopepsin-13.4.23.200.440
3ad9NADSubunit alpha of sarocosine oxidase/0.440
3bk2U5PRibonuclease J/0.440
3gwfNAPCyclohexanone monooxygenase/0.440
3lqfNADGalactitol dehydrogenase/0.440
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3ruaNADUDP-N-acetylglucosamine 4-epimerase/0.440
3vt7VDXVitamin D3 receptor/0.440
4j0v1H7Beta-secretase 13.4.23.460.440