Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
2bb3SAHCobalamin biosynthesis precorrin-6Y methylase (CbiE)

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2bb3SAHCobalamin biosynthesis precorrin-6Y methylase (CbiE)/1.000
2qbuSAHPrecorrin-2 methyltransferase/0.512
2gv8NDPThiol-specific monooxygenase1.14.130.488
1x1aSAMC-20 methyltransferase/0.486
1x1bSAHC-20 methyltransferase/0.486
2oapANPType II secretion system protein (GspE-2)/0.485
1szgFNSCytochrome b2, mitochondrial1.1.2.30.481
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.480
4yxm2BADNA integrity scanning protein DisA/0.480
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.479
2pncCLUPrimary amine oxidase, liver isozyme/0.476
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.476
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.474
4kbyC2EStimulator of interferon genes protein/0.474
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.473
4xguADPPutative pachytene checkpoint protein 2/0.473
4g74FADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.472
1x27ASP_TYR_VAL_HIS_PTRTyrosine-protein kinase Lck2.7.10.20.471
1w6hTITPlasmepsin-23.4.23.390.470
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.470
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.469
1xe55FEPlasmepsin-23.4.23.390.469
2c20NADUDP-glucose 4-epimerase/0.469
2ek7SAHDiphthine synthase/0.469
3f03FMNPentaerythritol tetranitrate reductase/0.469
3sxjSAMPutative methyltransferase/0.468
4irnFADAnaB/0.468
4xr9NADCalS8/0.468
3tjzGNPADP-ribosylation factor 1/0.467
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.466
3zvmADPBifunctional polynucleotide phosphatase/kinase2.7.1.780.466
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.465
2il2LIXRenin3.4.23.150.465
2lfoGCHFatty acid-binding protein, liver/0.465
3muoZPRProlyl endopeptidase/0.465
4nv10FXFormyl transferase/0.465
4qxr1YEStimulator of interferon genes protein/0.465
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.464
3hl0NADMaleylacetate reductase/0.464
3qt62P0Mevalonate diphosphate decarboxylase/0.464
4eb7PLPCysteine desulfurase IscS 2/0.464
4ohwATPProtein clpf-1/0.464
4q0kGA3Phytohormone-binding protein/0.464
2bu9HFVIsopenicillin N synthase1.21.3.10.463
1b2lNDCAlcohol dehydrogenase1.1.1.10.462
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.462
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.462
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.462
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.462
2pb4SAHDiphthine synthase/0.461
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.461
4x7uZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.461
1icqFMN12-oxophytodienoate reductase 11.3.1.420.460
1x1dSAHC-20 methyltransferase/0.460
2jb4A14Isopenicillin N synthase1.21.3.10.460
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.460
4b4vL34Bifunctional protein FolD/0.460
4dbzNDPPutative ketoacyl reductase1.3.10.460
1lbcCYZGlutamate receptor 2/0.459
2a94AP0L-lactate dehydrogenase1.1.1.270.459
2g1s4IGRenin3.4.23.150.459
2vbdV10Isopenicillin N synthase1.21.3.10.459
3kpbSAMUncharacterized protein MJ0100/0.459
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.459
2dxvSAHDiphthine synthase/0.458
2vkeTACTetracycline repressor protein class D/0.458
4df2FMNNADPH dehydrogenase/0.458
4zwmPLPOrnithine aminotransferase, mitochondrial, putative/0.458
1j1zATPArgininosuccinate synthase/0.457
2cy0NAPShikimate dehydrogenase (NADP(+))/0.457
2dftADPShikimate kinase2.7.1.710.457
2e07SAHDiphthine synthase/0.457
2i7pACOPantothenate kinase 32.7.1.330.457
2ifaFMNUncharacterized protein/0.457
2iviACWIsopenicillin N synthase1.21.3.10.457
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.457
2yd0BESEndoplasmic reticulum aminopeptidase 13.4.110.457
3h2sNDPPutative NADH-flavin reductase/0.457
3rpeFADPutative modulator of drug activity/0.457
4b65FADL-ornithine N(5)-monooxygenase/0.457
1amoFMNNADPH--cytochrome P450 reductase/0.456
1h73ANPHomoserine kinase2.7.1.390.456
1i5cADPChemotaxis protein CheA2.7.13.30.456
2g1n1IGRenin3.4.23.150.456
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.456
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.456
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.455
3gwfNAPCyclohexanone monooxygenase/0.455
3qe2FMNNADPH--cytochrome P450 reductase/0.455
4g6gFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.455
2cv2GSUGlutamate--tRNA ligase6.1.1.170.454
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.454
3gnvXNZGenome polyprotein2.7.7.480.454
3h3r14HCollagen type IV alpha-3-binding protein/0.454
3lqfNADGalactitol dehydrogenase/0.454
3pgtGBXGlutathione S-transferase P2.5.1.180.454
4bfvZVVPantothenate kinase2.7.1.330.454
4dpy2P0Mevalonate diphosphate decarboxylase/0.454
1icpFMN12-oxophytodienoate reductase 11.3.1.420.453
1j21ATPArgininosuccinate synthase/0.453
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.453
2o7oDXTTetracycline repressor protein class D/0.453
3h3qH13Collagen type IV alpha-3-binding protein/0.453
1bk0ACVIsopenicillin N synthase1.21.3.10.452
1h50FMNPentaerythritol tetranitrate reductase/0.452
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.452
1psa0ZLPepsin A3.4.23.10.452
1x1cSAHC-20 methyltransferase/0.452
2e8qSAHDiphthine synthase/0.452
2gevCOKPantothenate kinase2.7.1.330.452
3zkyWT4Isopenicillin N synthase1.21.3.10.452
4du82P0Mevalonate diphosphate decarboxylase/0.452
4rvgTYDD-mycarose 3-C-methyltransferase/0.452
1hb1OCVIsopenicillin N synthase1.21.3.10.451
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.451
2dv3SAHDiphthine synthase/0.451
2zvbSAHPrecorrin-3 C17-methyltransferase/0.451
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.451
1h2bNAJNAD-dependent alcohol dehydrogenase/0.450
1h63FMNPentaerythritol tetranitrate reductase/0.450
2ab8MTPAdenosine kinase2.7.1.200.450
2ed3SAHDiphthine synthase/0.450
2ed4NAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.450
2eh4SAHDiphthine synthase/0.450
2ejvNADL-threonine 3-dehydrogenase/0.450
3v0o4GWHisto-blood group ABO system transferase/0.450
4b63FADL-ornithine N(5)-monooxygenase/0.450
1culFOKAdenylate cyclase type 2/0.449
1culFOKAdenylate cyclase type 5/0.449
1hb3SCVIsopenicillin N synthase1.21.3.10.449
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.449
1xddAAYIntegrin alpha-L/0.449
2uxoTACHTH-type transcriptional regulator TtgR/0.449
3eksCY9Actin-5C/0.449
3f63GTXGlutathione transferase GST1-4/0.449
3ukoNADAlcohol dehydrogenase class-3/0.449
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.449
4q71FADBifunctional protein PutA/0.449
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.448
1pgtGTXGlutathione S-transferase P2.5.1.180.448
1rfvADPPyridoxal kinase2.7.1.350.448
1vjtNADAlpha-glucosidase, putative/0.448
2dsgSAHDiphthine synthase/0.448
2hsdNAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.448
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.448
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.448
4j4nD44Peptidylprolyl isomerase/0.448
5dp2NAPCurF/0.448
1opmIYGPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.447
1t2cNAIL-lactate dehydrogenase1.1.1.270.447
1xseNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
2g1y5IGRenin3.4.23.150.447
2pcmSAHDiphthine synthase/0.447
2rlcCHDCholoylglycine hydrolase3.5.1.240.447
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.447
3junAJDPhenazine biosynthesis protein A/B/0.447
3tr05GPGuanylate kinase/0.447
3vydVYDRenin3.4.23.150.447
5eioNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.447
2g226IGRenin3.4.23.150.446
2gesCOKPantothenate kinase2.7.1.330.446
3c3eGDP2-phospho-L-lactate transferase/0.446
3f3sNADLambda-crystallin homolog/0.446
4ambDUDPutative glycosyl transferase/0.446
4dc0NDPPutative ketoacyl reductase1.3.10.446
4g9kFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.446
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.446
4lcjNADC-terminal-binding protein 2/0.446
4tm1FDAKtzI/0.446
1touB1VFatty acid-binding protein, adipocyte/0.445
1vf3GDNGlutathione S-transferase 32.5.1.180.445
1xe65FPPlasmepsin-23.4.23.390.445
2dshSAHDiphthine synthase/0.445
2e16SAHDiphthine synthase/0.445
2emrSAHDiphthine synthase/0.445
2owgSAHDiphthine synthase/0.445
2qs1UB1Glutamate receptor ionotropic, kainate 1/0.445
2xtnGTPGTPase IMAP family member 2/0.445
3bl7DD1m7GpppX diphosphatase3.6.1.590.445
3fcjFADNitroalkane oxidase1.7.3.10.445
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.445
3skgPB8Beta-secretase 13.4.23.460.445
3tjlFMNNADPH dehydrogenase/0.445
4g3jVNTLanosterol 14-alpha-demethylase/0.445
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.444
1vceSAHDiphthine synthase/0.444
1yqzCOACoenzyme A disulfide reductase/0.444
2a2dANPN-acetylgalactosamine kinase2.7.1.1570.444
2eleSAHDiphthine synthase/0.444
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.444
2iibC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.444
2y60M8FIsopenicillin N synthase1.21.3.10.444
3zeiAWHO-acetylserine sulfhydrylase/0.444
4de2DN3Beta-lactamase/0.444
4rvfTYDD-mycarose 3-C-methyltransferase/0.444
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.443
2en5SAHDiphthine synthase/0.443
2g247IGRenin3.4.23.150.443
2huxSAHDiphthine synthase/0.443
2q1tNADPutative nucleotide sugar epimerase/ dehydratase/0.443
4bjzFADProbable salicylate monooxygenase/0.443
4oztP1AEcdysone receptor, putative/0.443
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.442
1ppjANYCytochrome b/0.442
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.442
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.442
2g1r3IGRenin3.4.23.150.442
2omeNADC-terminal-binding protein 2/0.442
2xpwOTCTetracycline repressor protein class D/0.442
3fr5I4AFatty acid-binding protein, adipocyte/0.442
3nutSAHPrecorrin-3 methylase/0.442
3udn09BBeta-secretase 13.4.23.460.442
3wqmB29Diterpene synthase3.1.7.80.442
3zkiWZVBeta-secretase 23.4.23.450.442
4b1e6T6Beta-secretase 13.4.23.460.442
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.442
4loi1YCStimulator of interferon genes protein/0.442
4lol1YEStimulator of interferon genes protein/0.442
1udyFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.441
2ag5NAD3-hydroxybutyrate dehydrogenase type 2/0.441
2dxwSAHDiphthine synthase/0.441
2emuSAHDiphthine synthase/0.441
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.441
4eqrCOACoenzyme A disulfide reductase/0.441
4qxq1YEStimulator of interferon genes protein/0.441
5d3qGDPDynamin-13.6.5.50.441
5dw50T1Succinyl-CoA:acetate CoA-transferase/0.441
1d0lBLGMembrane-bound lytic murein transglycosylase B4.2.2.n10.440
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.440
1mjbACOHistone acetyltransferase ESA1/0.440
1uzwCDHIsopenicillin N synthase1.21.3.10.440
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.440
2d3aADPGlutamine synthetase root isozyme 36.3.1.20.440
2hs6FMN12-oxophytodienoate reductase 31.3.1.420.440
2pb6SAHDiphthine synthase/0.440
2pchSAHDiphthine synthase/0.440
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.440
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.440
3mk6ACOPantothenate kinase 32.7.1.330.440
3zoiM2WIsopenicillin N synthase1.21.3.10.440
4b63NAPL-ornithine N(5)-monooxygenase/0.440
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.440
4gid0GHBeta-secretase 13.4.23.460.440
4i9n1E5L-lactate dehydrogenase A chain1.1.1.270.440