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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
2z6rSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2z6rSAHDiphthine synthase/1.000
2e17SAHDiphthine synthase/0.842
2ek2SAHDiphthine synthase/0.834
2owuSAHDiphthine synthase/0.814
2e07SAHDiphthine synthase/0.804
2ed5SAHDiphthine synthase/0.787
2eeqSAHDiphthine synthase/0.784
2e4nSAHDiphthine synthase/0.783
1wngSAHDiphthine synthase/0.776
2el0SAHDiphthine synthase/0.763
2pb6SAHDiphthine synthase/0.754
2e15SAHDiphthine synthase/0.750
2dv4SAHDiphthine synthase/0.749
2hutSAHDiphthine synthase/0.748
2huqSAHDiphthine synthase/0.747
2eh4SAHDiphthine synthase/0.744
2huvSAHDiphthine synthase/0.744
2dsiSAHDiphthine synthase/0.743
2owkSAHDiphthine synthase/0.728
2ejjSAHDiphthine synthase/0.721
2ek3SAHDiphthine synthase/0.720
2pcaSAHDiphthine synthase/0.718
2p9dSAHDiphthine synthase/0.712
2el3SAHDiphthine synthase/0.706
2eh2SAHDiphthine synthase/0.705
2owgSAHDiphthine synthase/0.703
2dekSAHDiphthine synthase/0.695
2dv7SAHDiphthine synthase/0.695
2p6kSAHDiphthine synthase/0.689
2dv5SAHDiphthine synthase/0.685
2p6iSAHDiphthine synthase/0.685
2ek4SAHDiphthine synthase/0.684
2p5fSAHDiphthine synthase/0.681
2dxwSAHDiphthine synthase/0.679
2eldSAHDiphthine synthase/0.679
2eniSAHDiphthine synthase/0.675
2p6lSAHDiphthine synthase/0.674
2p5cSAHDiphthine synthase/0.672
2ed3SAHDiphthine synthase/0.670
2pb5SAHDiphthine synthase/0.668
2emrSAHDiphthine synthase/0.667
2ehlSAHDiphthine synthase/0.666
2dsgSAHDiphthine synthase/0.665
2dshSAHDiphthine synthase/0.664
2dv3SAHDiphthine synthase/0.660
2e8rSAHDiphthine synthase/0.658
2emuSAHDiphthine synthase/0.656
2dxxSAHDiphthine synthase/0.655
1vceSAHDiphthine synthase/0.650
2hr8SAHDiphthine synthase/0.648
2huxSAHDiphthine synthase/0.647
2ejkSAHDiphthine synthase/0.645
2eh5SAHDiphthine synthase/0.641
2pckSAHDiphthine synthase/0.639
2dxvSAHDiphthine synthase/0.637
2e8sSAHDiphthine synthase/0.634
2p2xSAHDiphthine synthase/0.634
2pciSAHDiphthine synthase/0.634
2e8hSAHDiphthine synthase/0.631
2e8qSAHDiphthine synthase/0.629
2owvSAHDiphthine synthase/0.626
2pb4SAHDiphthine synthase/0.612
2pchSAHDiphthine synthase/0.611
2e08SAHDiphthine synthase/0.610
2e7rSAHDiphthine synthase/0.607
2e16SAHDiphthine synthase/0.594
2ek7SAHDiphthine synthase/0.594
2egbSAHDiphthine synthase/0.589
2eglSAHDiphthine synthase/0.587
2egsSAHDiphthine synthase/0.587
2p6dSAHDiphthine synthase/0.584
2pcmSAHDiphthine synthase/0.583
2ejzSAHDiphthine synthase/0.578
2en5SAHDiphthine synthase/0.578
2owfSAHDiphthine synthase/0.578
2eleSAHDiphthine synthase/0.577
2pcgSAHDiphthine synthase/0.568
2ekaSAHDiphthine synthase/0.567
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.505
1xe55FEPlasmepsin-23.4.23.390.493
2gjlFMNNitronate monooxygenase1.13.12.160.486
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.486
1g63FMNEpidermin decarboxylase4.1.10.480
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.480
4dpuAGSMevalonate diphosphate decarboxylase/0.480
3gw9VNILanosterol 14-alpha-demethylase/0.477
3wv9FEGHmd co-occurring protein HcgE/0.477
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.476
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.476
4bfzZVZPantothenate kinase2.7.1.330.474
2ifaFMNUncharacterized protein/0.473
2rlcCHDCholoylglycine hydrolase3.5.1.240.473
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.473
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.473
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.473
2q5g1FAPeroxisome proliferator-activated receptor delta/0.472
1tj0FADBifunctional protein PutA1.5.5.20.471
1dirNADDihydropteridine reductase1.5.1.340.470
3ijoB4DGlutamate receptor 2/0.470
3pqbVGPPutative oxidoreductase/0.469
1lbcCYZGlutamate receptor 2/0.468
1pjcNADAlanine dehydrogenase/0.468
4tm3FADKtzI/0.468
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.467
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
3s1dZIRCytokinin dehydrogenase 11.5.99.120.466
3vqsJT1Genome polyprotein/0.465
4a83DXCMajor pollen allergen Bet v 1-A/0.464
1tqf32PBeta-secretase 13.4.23.460.463
1vp6CMPCyclic nucleotide-gated potassium channel mll3241/0.463
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
1dhrNADDihydropteridine reductase1.5.1.340.462
1me6IVSPlasmepsin-23.4.23.390.462
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.462
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
5f8eSAHPossible transcriptional regulatory protein/0.462
2q4bNAPUncharacterized protein At5g02240/0.461
4bfxZVXPantothenate kinase2.7.1.330.461
1a72PADAlcohol dehydrogenase E chain1.1.1.10.460
2bjfDXCCholoylglycine hydrolase3.5.1.240.460
3a3gDLZLumazine protein/0.460
1orrNADCDP-paratose 2-epimerase/0.459
2a94AP0L-lactate dehydrogenase1.1.1.270.459
3wb2YGPUncharacterized protein MJ0488/0.459
4a8v2ANMajor pollen allergen Bet v 1-J/0.459
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.458
2gv8NDPThiol-specific monooxygenase1.14.130.458
2uxoTACHTH-type transcriptional regulator TtgR/0.458
4dpy2P0Mevalonate diphosphate decarboxylase/0.458
4i8zG08Gag-Pol polyprotein3.4.23.160.458
5c77SAHProtein arginine N-methyltransferase SFM1/0.458
1ep3FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.457
1hdrNADDihydropteridine reductase1.5.1.340.457
1t2cNAIL-lactate dehydrogenase1.1.1.270.457
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.457
4g3jVNTLanosterol 14-alpha-demethylase/0.457
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.457
2b53D23Cyclin-dependent kinase 22.7.11.220.456
2fznFADBifunctional protein PutA1.5.5.20.456
3gwfNAPCyclohexanone monooxygenase/0.456
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.456
1f8fNADBenzyl alcohol dehydrogenase/0.455
1w6hTITPlasmepsin-23.4.23.390.455
2bu9HFVIsopenicillin N synthase1.21.3.10.455
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.455
2h9iEADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.455
2he5NDPAldo-keto reductase family 1 member C211.1.10.455
3omuIBDHeat shock protein 83/0.455
1bwsNDPGDP-L-fucose synthase/0.454
3ig6438Urokinase-type plasminogen activator3.4.21.730.454
4g7gVFVLanosterol 14-alpha-demethylase/0.454
4m83ERYOleandomycin glycosyltransferase2.4.10.454
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.453
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.453
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.453
3h3sH15Collagen type IV alpha-3-binding protein/0.453
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.453
4du82P0Mevalonate diphosphate decarboxylase/0.453
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.453
1udaUFGUDP-glucose 4-epimerase5.1.3.20.452
1udbUFGUDP-glucose 4-epimerase5.1.3.20.452
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.452
2givACOHistone acetyltransferase KAT8/0.452
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.452
3pxkPXKFocal adhesion kinase 12.7.10.20.452
3r9uFADThioredoxin reductase/0.452
4ji91M3Tyrosine-protein kinase JAK2/0.452
5hwsNAP2-dehydropantoate 2-reductase/0.452
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.451
1ma0NADAlcohol dehydrogenase class-31.1.1.10.451
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.451
1z1fSTLResveratrol synthase/0.451
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.451
2jb4A14Isopenicillin N synthase1.21.3.10.451
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.451
1f20FADNitric oxide synthase, brain1.14.13.390.450
1juvNDPDihydrofolate reductase1.5.1.30.450
1pd9CO4Dihydrofolate reductase1.5.1.30.450
1udyFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.450
1xe65FPPlasmepsin-23.4.23.390.450
2y3sTIRTamL/0.450
3h06VBPGlutamate receptor 2/0.450
3lqfNADGalactitol dehydrogenase/0.450
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.450
1kp3ATPArgininosuccinate synthase6.3.4.50.449
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.449
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3hl0NADMaleylacetate reductase/0.449
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4irnFADAnaB/0.449
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.448
1qoqIGPTryptophan synthase alpha chain/0.448
1xddAAYIntegrin alpha-L/0.448
1zemNADXylitol dehydrogenase/0.448
2aqkNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.448
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3qwbNDPProbable quinone oxidoreductase1.6.5.50.448
4ejvLCLTranscriptional regulator TcaR/0.448
4j0v1H7Beta-secretase 13.4.23.460.448
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
4q71FADBifunctional protein PutA/0.448
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.448
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
5af7FADAcyl-CoA dehydrogenase/0.448
1fm4DXCMajor pollen allergen Bet v 1-L/0.447
2w06FRVCyclin-dependent kinase 22.7.11.220.447
3qgf46FGenome polyprotein2.7.7.480.447
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.447
4a81DXCMajor pollen allergen Bet v 1-A/0.447
4djy0KRBeta-secretase 13.4.23.460.447
4kugNAD3-hydroxybutyryl-CoA dehydrogenase/0.447
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1x1bSAHC-20 methyltransferase/0.446
2gtbAZPOrf1ab polyprotein/0.446
2rhgIGPTryptophan synthase alpha chain/0.446
2w3bNDPDihydrofolate reductase1.5.1.30.446
2zvbSAHPrecorrin-3 C17-methyltransferase/0.446
3enkUPGUDP-glucose 4-epimerase/0.446
3vf30GSBeta-secretase 13.4.23.460.446
4eb7PLPCysteine desulfurase IscS 2/0.446
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.446
5dp2NAPCurF/0.446
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.445
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.445
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
4egbNADdTDP-glucose 4,6-dehydratase/0.445
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.445
4prvADPDNA gyrase subunit B/0.445
5koiNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.445
1cbfSAHCobalt-precorrin-4 C(11)-methyltransferase2.1.1.2710.444
1t88CAMCamphor 5-monooxygenase1.14.15.10.444
1x1aSAMC-20 methyltransferase/0.444
1yqzCOACoenzyme A disulfide reductase/0.444
2gz7D3FOrf1a polyprotein/0.444
2vhzNAIAlanine dehydrogenase1.4.1.10.444
3e8nVRADual specificity mitogen-activated protein kinase kinase 12.7.12.20.444
4a802ANMajor pollen allergen Bet v 1-A/0.444
4b1rITCTetracycline repressor protein class D/0.444
4bftZVTPantothenate kinase2.7.1.330.444
4bfvZVVPantothenate kinase2.7.1.330.444
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.444
1g1aNADdTDP-glucose 4,6-dehydratase/0.443
1qjfACSIsopenicillin N synthase1.21.3.10.443
2fzwNADAlcohol dehydrogenase class-31.1.1.10.443
2p3b3TLV-1 PROTEASE protein/0.443
2p3b3TLV-1 protease/0.443
2qbuSAHPrecorrin-2 methyltransferase/0.443
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.443
2vwqNAPGlucose 1-dehydrogenase/0.443
2xc3RT8Steroid C26-monooxygenase1.14.13.1410.443
3a3yOBNSodium/potassium-transporting ATPase subunit alpha/0.443
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
3d5m4MSGenome polyprotein2.7.7.480.443
3d8vUD1Bifunctional protein GlmU/0.443
3kb1ADPIron-sulfur cluster carrier protein/0.443
3lsiFADPyranose 2-oxidase/0.443
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.443
3nutSAHPrecorrin-3 methylase/0.443
4cukNAID-lactate dehydrogenase/0.443
4dxd9PCCell division protein FtsZ/0.443
4f5yC2EStimulator of interferon genes protein/0.443
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.443
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4nakPBQ2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic2.7.7.600.443
1f8wFADNADH peroxidase1.11.1.10.442
1qorNDPQuinone oxidoreductase 1/0.442
1xl5190Gag-Pol polyprotein3.4.23.160.442
1y0s331Peroxisome proliferator-activated receptor delta/0.442
1zeoC01Peroxisome proliferator-activated receptor gamma/0.442
2oapANPType II secretion system protein (GspE-2)/0.442
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.442
3sf6FDAGlutaryl-CoA dehydrogenase/0.442
3wagTYDGlycosyltransferase/0.442
4bb3KKAIsopenicillin N synthase1.21.3.10.442
4qecNAPElxO/0.442
1k7fIAVTryptophan synthase alpha chain/0.441
1nhhANPDNA mismatch repair protein MutL/0.441
1y4lSVRBasic phospholipase A2 homolog 2/0.441
2a1tFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.441
2bn4FMNNADPH--cytochrome P450 reductase/0.441
2g226IGRenin3.4.23.150.441
2pobGW4Peroxisome proliferator-activated receptor gamma/0.441
3ad9NADSubunit alpha of sarocosine oxidase/0.441
3d84NDPDihydrofolate reductase1.5.1.30.441
3gqvNAPEnoyl reductase LovC10.441
3kc3MK2MAP kinase-activated protein kinase 22.7.11.10.441
3qt62P0Mevalonate diphosphate decarboxylase/0.441
3uylTYDProbable NDP-rhamnosyltransferase/0.441
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.441
4ejmNAPPutative zinc-binding dehydrogenase/0.441
4h3j10WBeta-secretase 13.4.23.460.441
4wudANPDNA gyrase subunit B/0.441
1bim0QBRenin3.4.23.150.440
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1o97FADElectron transfer flavoprotein subunit alpha/0.440
1t9gFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.440
1u3cFADCryptochrome-1/0.440
1uzwCDHIsopenicillin N synthase1.21.3.10.440
2ien017Gag-Pol polyprotein3.4.23.160.440
2p5uNADUDP-glucose 4-epimerase/0.440
3dh7FMNIsopentenyl-diphosphate delta-isomerase/0.440
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.440
3nl6TPSUncharacterized protein/0.440
3to6LYS_CMCHistone acetyltransferase ESA1/0.440
3vvpBNUUncharacterized protein/0.440
3vx4ATPPutative ABC transporter, ATP-binding protein ComA/0.440
4fv7E94Mitogen-activated protein kinase 12.7.11.240.440
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA23.6.30.440
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA1/0.440
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.440