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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
2p2xSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2p2xSAHDiphthine synthase/1.000
2p5fSAHDiphthine synthase/0.837
2p5cSAHDiphthine synthase/0.806
2egsSAHDiphthine synthase/0.805
2ejkSAHDiphthine synthase/0.796
2ed5SAHDiphthine synthase/0.780
2dxwSAHDiphthine synthase/0.773
2p6kSAHDiphthine synthase/0.772
2dxvSAHDiphthine synthase/0.766
2egbSAHDiphthine synthase/0.760
2owkSAHDiphthine synthase/0.760
2owuSAHDiphthine synthase/0.749
2dxxSAHDiphthine synthase/0.743
2e7rSAHDiphthine synthase/0.743
2ekaSAHDiphthine synthase/0.739
2dsiSAHDiphthine synthase/0.736
2eniSAHDiphthine synthase/0.734
2dv7SAHDiphthine synthase/0.732
2emrSAHDiphthine synthase/0.732
2dv5SAHDiphthine synthase/0.722
2pb5SAHDiphthine synthase/0.721
2owgSAHDiphthine synthase/0.715
2el0SAHDiphthine synthase/0.713
2p6dSAHDiphthine synthase/0.713
2pcgSAHDiphthine synthase/0.710
2eh2SAHDiphthine synthase/0.709
2pcmSAHDiphthine synthase/0.709
2eglSAHDiphthine synthase/0.708
2e08SAHDiphthine synthase/0.698
2e8sSAHDiphthine synthase/0.698
2p6iSAHDiphthine synthase/0.695
2dv4SAHDiphthine synthase/0.691
2pckSAHDiphthine synthase/0.691
2eh5SAHDiphthine synthase/0.690
2hutSAHDiphthine synthase/0.689
2e8qSAHDiphthine synthase/0.683
2ehlSAHDiphthine synthase/0.682
2pchSAHDiphthine synthase/0.681
2pb4SAHDiphthine synthase/0.678
2ek3SAHDiphthine synthase/0.674
2ek7SAHDiphthine synthase/0.671
2emuSAHDiphthine synthase/0.671
2p9dSAHDiphthine synthase/0.668
2huvSAHDiphthine synthase/0.667
2dsgSAHDiphthine synthase/0.666
2eleSAHDiphthine synthase/0.666
2hr8SAHDiphthine synthase/0.665
2en5SAHDiphthine synthase/0.656
2pcaSAHDiphthine synthase/0.655
2eeqSAHDiphthine synthase/0.653
1vceSAHDiphthine synthase/0.647
2ejjSAHDiphthine synthase/0.647
1wngSAHDiphthine synthase/0.640
2e16SAHDiphthine synthase/0.638
2e17SAHDiphthine synthase/0.638
2e07SAHDiphthine synthase/0.637
2pciSAHDiphthine synthase/0.635
2e15SAHDiphthine synthase/0.634
2z6rSAHDiphthine synthase/0.634
2huxSAHDiphthine synthase/0.630
2ek2SAHDiphthine synthase/0.629
2dshSAHDiphthine synthase/0.628
2owvSAHDiphthine synthase/0.624
2eh4SAHDiphthine synthase/0.622
2e4nSAHDiphthine synthase/0.619
2huqSAHDiphthine synthase/0.611
2e8rSAHDiphthine synthase/0.609
2dv3SAHDiphthine synthase/0.604
2e8hSAHDiphthine synthase/0.601
2dekSAHDiphthine synthase/0.598
2pb6SAHDiphthine synthase/0.589
2ed3SAHDiphthine synthase/0.584
2owfSAHDiphthine synthase/0.582
2el3SAHDiphthine synthase/0.578
2ek4SAHDiphthine synthase/0.574
2eldSAHDiphthine synthase/0.553
2ejzSAHDiphthine synthase/0.539
2p6lSAHDiphthine synthase/0.539
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.496
2y3sTIRTamL/0.487
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.485
3gw9VNILanosterol 14-alpha-demethylase/0.484
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.483
3ijoB4DGlutamate receptor 2/0.478
1g63FMNEpidermin decarboxylase4.1.10.477
4dbzNDPPutative ketoacyl reductase1.3.10.475
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.474
1lbcCYZGlutamate receptor 2/0.473
1pd9CO4Dihydrofolate reductase1.5.1.30.473
2pj4414Carboxypeptidase B/0.473
2xhd7T9Glutamate receptor 2/0.473
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.471
1x1cSAHC-20 methyltransferase/0.470
3ig6438Urokinase-type plasminogen activator3.4.21.730.470
1bim0QBRenin3.4.23.150.468
1dirNADDihydropteridine reductase1.5.1.340.468
3to6LYS_CMCHistone acetyltransferase ESA1/0.468
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.467
1g1aNADdTDP-glucose 4,6-dehydratase/0.466
1v9aSAHUncharacterized protein/0.466
2p5uNADUDP-glucose 4-epimerase/0.466
3vqsJT1Genome polyprotein/0.466
4g7gVFVLanosterol 14-alpha-demethylase/0.466
4g3jVNTLanosterol 14-alpha-demethylase/0.465
4r21STRCytochrome P450 family 17 polypeptide 2/0.465
2wo7ASVIsopenicillin N synthase1.21.3.10.463
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.463
4xguADPPutative pachytene checkpoint protein 2/0.463
1x1dSAHC-20 methyltransferase/0.462
2am22LGUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.462
3otwCOAPhosphopantetheine adenylyltransferase/0.462
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.462
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.461
4b1rITCTetracycline repressor protein class D/0.461
4wriOKAOkadaic acid binding protein 2-alpha/0.461
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.460
1xddAAYIntegrin alpha-L/0.460
3c1y2BADNA integrity scanning protein DisA/0.460
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.460
4h3j10WBeta-secretase 13.4.23.460.460
4m83ERYOleandomycin glycosyltransferase2.4.10.460
1zeoC01Peroxisome proliferator-activated receptor gamma/0.459
2rcyNAPPyrroline-5-carboxylate reductase/0.459
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.459
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
4xumIMNPeroxisome proliferator-activated receptor gamma/0.459
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.459
2gjlFMNNitronate monooxygenase1.13.12.160.458
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.458
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.458
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.458
4acxS8ZBeta-secretase 13.4.23.460.458
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.458
2xx91NFGlutamate receptor 2/0.457
3d8bADPFidgetin-like protein 13.6.40.457
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.457
3zh8C58Protein kinase C iota type2.7.11.130.457
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.457
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.456
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.456
3nutSAHPrecorrin-3 methylase/0.456
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.456
4a8v2ANMajor pollen allergen Bet v 1-J/0.456
4i1iNADMalate dehydrogenase/0.456
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.456
2uxoTACHTH-type transcriptional regulator TtgR/0.455
4djy0KRBeta-secretase 13.4.23.460.455
4iwq1FVSerine/threonine-protein kinase TBK12.7.11.10.455
1f20FADNitric oxide synthase, brain1.14.13.390.454
1xe55FEPlasmepsin-23.4.23.390.454
1xe65FPPlasmepsin-23.4.23.390.453
2givACOHistone acetyltransferase KAT8/0.453
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.453
3bc3OPTCathepsin L13.4.22.150.453
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.453
3tneRITCandidapepsin-13.4.23.240.453
4bfxZVXPantothenate kinase2.7.1.330.453
2irzI02Beta-secretase 13.4.23.460.452
3kb1ADPIron-sulfur cluster carrier protein/0.452
3wmxNADNAD dependent epimerase/dehydratase/0.452
4tuvCPZCytochrome P450 1191.140.452
4zohFADPutative oxidoreductase FAD-binding subunit/0.452
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.451
2vkeTACTetracycline repressor protein class D/0.451
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.451
3vt7VDXVitamin D3 receptor/0.451
4dpuAGSMevalonate diphosphate decarboxylase/0.451
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.451
1k7fIAVTryptophan synthase alpha chain/0.450
2rlcCHDCholoylglycine hydrolase3.5.1.240.450
2vcmM11Isopenicillin N synthase1.21.3.10.450
2zb3NDPProstaglandin reductase 21.3.1.480.450
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3lqfNADGalactitol dehydrogenase/0.450
3pxkPXKFocal adhesion kinase 12.7.10.20.450
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.450
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.449
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1t2cNAIL-lactate dehydrogenase1.1.1.270.449
1tj0FADBifunctional protein PutA1.5.5.20.449
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.449
3ox4NADAlcohol dehydrogenase 21.1.1.10.449
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.449
1mj9COAHistone acetyltransferase ESA1/0.448
1mp0NADAlcohol dehydrogenase class-31.1.1.10.448
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.448
1x1aSAMC-20 methyltransferase/0.448
2a94AP0L-lactate dehydrogenase1.1.1.270.448
2b53D23Cyclin-dependent kinase 22.7.11.220.448
2he5NDPAldo-keto reductase family 1 member C211.1.10.448
2q7vFADThioredoxin reductase/0.448
3a1nNADNDP-sugar epimerase/0.448
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3hl0NADMaleylacetate reductase/0.448
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4bb3KKAIsopenicillin N synthase1.21.3.10.448
4dx9SER_ALA_VAL_THRIntegrin beta-1/0.448
4dx9SER_ALA_VAL_THRIntegrin beta-1-binding protein 1/0.448
4ejmNAPPutative zinc-binding dehydrogenase/0.448
1bxoPP7Penicillopepsin-13.4.23.200.447
1f8fNADBenzyl alcohol dehydrogenase/0.447
1obnASVIsopenicillin N synthase1.21.3.10.447
1pjcNADAlanine dehydrogenase/0.447
1y0s331Peroxisome proliferator-activated receptor delta/0.447
2iyfERYOleandomycin glycosyltransferase2.4.10.447
2q5g1FAPeroxisome proliferator-activated receptor delta/0.447
2qzlIXSBeta-secretase 13.4.23.460.447
3wb2YGPUncharacterized protein MJ0488/0.447
4irnFADAnaB/0.447
4nbwNADShort-chain dehydrogenase/reductase SDR/0.447
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.446
1szmBI4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
1yb5NAPQuinone oxidoreductase1.6.5.50.446
2dftADPShikimate kinase2.7.1.710.446
2ep7NADGlyceraldehyde-3-phosphate dehydrogenase/0.446
2oapANPType II secretion system protein (GspE-2)/0.446
2ou2ACOHistone acetyltransferase KAT5/0.446
2ozuACOHistone acetyltransferase KAT6A/0.446
2q4bNAPUncharacterized protein At5g02240/0.446
3d91REMRenin3.4.23.150.446
3il1B5DGlutamate receptor 2/0.446
3mjrAC2Deoxycytidine kinase2.7.1.740.446
3pb3SAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.446
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.446
4b7754MBeta-secretase 13.4.23.460.446
4fv7E94Mitogen-activated protein kinase 12.7.11.240.446
4h3f10OBeta-secretase 13.4.23.460.446
4wudANPDNA gyrase subunit B/0.446
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.446
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.445
1vp6CMPCyclic nucleotide-gated potassium channel mll3241/0.445
2gv8NDPThiol-specific monooxygenase1.14.130.445
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.445
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.445
3gwfNAPCyclohexanone monooxygenase/0.445
3slkNDPPolyketide synthase extender module 2/0.445
3tkiS25Serine/threonine-protein kinase Chk12.7.11.10.445
3zoiM2WIsopenicillin N synthase1.21.3.10.445
4bf2STUMitogen-activated protein kinase kinase kinase 52.7.11.250.445
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.445
1kkq471Peroxisome proliferator-activated receptor alpha/0.444
1q8wM77cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
1tqf32PBeta-secretase 13.4.23.460.444
2p8hMY9Beta-secretase 13.4.23.460.444
2znq401Peroxisome proliferator-activated receptor delta/0.444
3a3gDLZLumazine protein/0.444
3adaNADSubunit alpha of sarocosine oxidase/0.444
3umpATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.444
3zkyWT4Isopenicillin N synthase1.21.3.10.444
4q71FADBifunctional protein PutA/0.444
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.444
1blzACVIsopenicillin N synthase1.21.3.10.443
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.443
1ma0NADAlcohol dehydrogenase class-31.1.1.10.443
1xefATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.443
2ahrNAPPyrroline-5-carboxylate reductase/0.443
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
2g1s4IGRenin3.4.23.150.443
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.443
2v7qATPATP synthase subunit alpha, mitochondrial/0.443
2v7qATPATP synthase subunit beta, mitochondrial3.6.3.140.443
2zvbSAHPrecorrin-3 C17-methyltransferase/0.443
3kpkFADSulfide-quinone reductase/0.443
3oibFDAPutative acyl-CoA dehydrogenase/0.443
3pqbVGPPutative oxidoreductase/0.443
3r95ACOMccE protein/0.443
4f5yC2EStimulator of interferon genes protein/0.443
4n9iPCGCatabolite expression activator/0.443
1dhrNADDihydropteridine reductase1.5.1.340.442
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1me6IVSPlasmepsin-23.4.23.390.442
1mjaCOAHistone acetyltransferase ESA1/0.442
1nhhANPDNA mismatch repair protein MutL/0.442
1vikBAYGag-Pol polyprotein/0.442
2fznFADBifunctional protein PutA1.5.5.20.442
2fzwNADAlcohol dehydrogenase class-31.1.1.10.442
2po7CHDFerrochelatase, mitochondrial4.99.1.10.442
2qbuSAHPrecorrin-2 methyltransferase/0.442
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3i59N6RCRP-like cAMP-activated global transcriptional regulator/0.442
3qfrFMNNADPH--cytochrome P450 reductase/0.442
3sdkP3NProteasome subunit beta type-53.4.25.10.442
3sdkP3NProteasome subunit beta type-63.4.25.10.442
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.442
4m4922YL-lactate dehydrogenase A chain1.1.1.270.442
4rquNADAlcohol dehydrogenase class-P/0.442
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1omoNADAlanine dehydrogenase/0.441
2cig1DGDihydrofolate reductase1.5.1.30.441
2fgjATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.441
2fgkATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.441
2ifaFMNUncharacterized protein/0.441
2q61SF1Peroxisome proliferator-activated receptor gamma/0.441
2w06FRVCyclin-dependent kinase 22.7.11.220.441
3clrFADElectron transfer flavoprotein subunit alpha/0.441
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.441
3ixj586Beta-secretase 13.4.23.460.441
3mdmFJZCholesterol 24-hydroxylase/0.441
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.441
3sufSUEPolyprotein/0.441
4aw1ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.441
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.441
4enhFVXCholesterol 24-hydroxylase/0.441
5a3cNADSIR2 family protein/0.441
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.440
1x1bSAHC-20 methyltransferase/0.440
1zioAP5Adenylate kinase/0.440
2bjfDXCCholoylglycine hydrolase3.5.1.240.440
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.440
2jj2ANPATP synthase subunit beta, mitochondrial3.6.3.140.440
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.440
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.440
3hdmMMGSerine/threonine-protein kinase Sgk12.7.11.10.440
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.440
3ixp834Ecdysone receptor/0.440
3lu1NADUDP-N-acetylglucosamine 4-epimerase/0.440
3so9017Pol protein/0.440
3u9eCOALmo1369 protein/0.440
4dc0NDPPutative ketoacyl reductase1.3.10.440
4frkDWDBeta-secretase 13.4.23.460.440
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.440
4yaoFMNNADPH--cytochrome P450 reductase/0.440
5hwsNAP2-dehydropantoate 2-reductase/0.440