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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
3oiiSAHRibosomal RNA small subunit methyltransferase NEP1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3oiiSAHRibosomal RNA small subunit methyltransferase NEP1/1.000
3oijSAHRibosomal RNA small subunit methyltransferase NEP1/0.598
3o7bSAHRibosomal RNA small subunit methyltransferase Nep1/0.499
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.498
3bbhSFGRibosomal RNA small subunit methyltransferase Nep12.1.10.495
1kp3ATPArgininosuccinate synthase6.3.4.50.489
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.485
1xh7R96cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.484
2zz0FADThioredoxin reductase 1, cytoplasmic1.8.1.90.483
4xczFONQdtf/0.483
3bbdSAHRibosomal RNA small subunit methyltransferase Nep12.1.10.482
4jwfSAHtRNA (guanine(9)-N1)-methyltransferase/0.482
2ien017Gag-Pol polyprotein3.4.23.160.481
5cyoGDPSeptin-9/0.481
4eb7PLPCysteine desulfurase IscS 2/0.479
1sveI01cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.478
3adaNADSubunit alpha of sarocosine oxidase/0.478
2uzwSS4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.476
3r83Z14Cyclin-dependent kinase 22.7.11.220.476
4l4fCAMCamphor 5-monooxygenase1.14.15.10.476
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.475
3fg2FADPutative rubredoxin reductase/0.472
4lol1YEStimulator of interferon genes protein/0.472
1fwkADPHomoserine kinase2.7.1.390.471
3s7dLEU_SER_LYS_LYS_MLZN-lysine methyltransferase SMYD2/0.471
4l4eCAMCamphor 5-monooxygenase1.14.15.10.471
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.468
4axaRKDcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.468
2iqgF2IBeta-secretase 13.4.23.460.467
1svgI04cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.466
2a1oCAMCamphor 5-monooxygenase1.14.15.10.466
4ke01R8Beta-secretase 13.4.23.460.466
1w6hTITPlasmepsin-23.4.23.390.465
2uw7GVPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.465
3nk7SAM23S rRNA (adenosine(1067)-2'-O)-methyltransferase/0.465
4i8zG08Gag-Pol polyprotein3.4.23.160.465
4yaoFMNNADPH--cytochrome P450 reductase/0.465
1f8wFADNADH peroxidase1.11.1.10.464
1xl5190Gag-Pol polyprotein3.4.23.160.464
4bkqNAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.464
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.464
3ag6PAJPantothenate synthetase/0.463
1owmFADDeoxyribodipyrimidine photo-lyase4.1.99.30.462
1bx6BA1cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.460
1hbvGANGag-Pol polyprotein/0.460
2rabFADGlutathione amide reductase/0.460
3fwjCAMCamphor 5-monooxygenase1.14.15.10.460
3pwm017Gag-Pol polyprotein3.4.23.160.460
3qfrFMNNADPH--cytochrome P450 reductase/0.460
2uw5GVNcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.459
2ylsFADPhenylacetone monooxygenase1.14.13.920.459
2ylzFADPhenylacetone monooxygenase1.14.13.920.459
3zeiAWHO-acetylserine sulfhydrylase/0.459
4eueNAITrans-2-enoyl-CoA reductase [NADH]/0.459
1lf3EH5Plasmepsin-23.4.23.390.458
1psa0ZLPepsin A3.4.23.10.458
2uzuL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.458
3isjA8DPantothenate synthetase6.3.2.10.458
3vyeVYERenin3.4.23.150.458
5ah5LSSLeucine--tRNA ligase/0.458
2rcyNAPPyrroline-5-carboxylate reductase/0.457
2uw0GVKcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.457
3e8eG98cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.457
3ioeA7DPantothenate synthetase6.3.2.10.457
4kkyCAMCamphor 5-monooxygenase1.14.15.10.457
4opuFDAConserved Archaeal protein/0.457
1ja0FMNNADPH--cytochrome P450 reductase/0.456
2ha8SAHProbable methyltransferase TARBP1/0.456
3bwjARXcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.456
3hztJ60Calmodulin-like domain protein kinase isoform 3/0.456
3vqhIQBcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.456
4mcc21XtRNA (guanine-N(1)-)-methyltransferase2.1.1.2280.456
1bdlIM1Gag-Pol polyprotein3.4.23.160.455
2uzlC94Cyclin-dependent kinase 22.7.11.220.455
3ckqUPGGlucosyl-3-phosphoglycerate synthase2.4.1.2660.455
3kb1ADPIron-sulfur cluster carrier protein/0.455
5cypGSPSeptin-9/0.455
5kwvANPPantothenate synthetase/0.455
1rejB1LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.454
1vikBAYGag-Pol polyprotein/0.454
3oqkS52Renin3.4.23.150.454
4dbzNDPPutative ketoacyl reductase1.3.10.454
2f2uM77Rho-associated protein kinase 22.7.11.10.453
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.453
2owfSAHDiphthine synthase/0.453
4q1x017Gag-Pol polyprotein3.4.23.160.453
1kfcIPLTryptophan synthase alpha chain/0.452
1n2jPAFPantothenate synthetase6.3.2.10.452
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.452
2dvlFADAcyl-CoA dehydrogenase/0.452
2i4qUA4Renin3.4.23.150.452
2p3b3TLV-1 PROTEASE protein/0.452
2p3b3TLV-1 protease/0.452
2uztSS3cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.452
2wsbNADGalactitol dehydrogenase/0.452
3fwfCAMCamphor 5-monooxygenase1.14.15.10.452
3nsh957Beta-secretase 13.4.23.460.452
4i0i957Beta-secretase 13.4.23.460.452
4jx1CAMCamphor 5-monooxygenase1.14.15.10.452
4yqfGDPSeptin-9/0.452
5eghPCEctonucleotide pyrophosphatase/phosphodiesterase family member 6/0.452
1t2cNAIL-lactate dehydrogenase1.1.1.270.451
1zrqFAD5,10-methylenetetrahydrofolate reductase1.5.1.200.451
2ed3SAHDiphthine synthase/0.451
2gu8796cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
3ai3NDPNADPH-sorbose reductase/0.451
3ivxFG6Pantothenate synthetase6.3.2.10.451
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.451
4loqSB4Mitogen-activated protein kinase 14/0.451
1c4yIH3Prothrombin3.4.21.50.450
2c1aI5ScAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
2ou5FMNPyridoxamine 5'-phosphate oxidase-related FMN-binding protein/0.450
2uzvSS5cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.450
3hwrNDP2-dehydropantoate 2-reductase/0.450
3pdqKC6Lysine-specific demethylase 4A1.14.110.450
3qzfX66Cyclin-dependent kinase 22.7.11.220.450
4a84DXCMajor pollen allergen Bet v 1-A/0.450
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.450
4ihl1F514-3-3 protein zeta/delta/0.450
4iv6FDAIsovaleryl-CoA dehydrogenase/0.450
1bxqPP8Penicillopepsin-13.4.23.200.449
1j9zFADNADPH--cytochrome P450 reductase/0.449
1tv8SAMGTP 3',8-cyclase4.1.99.180.449
1w4xFADPhenylacetone monooxygenase1.14.13.920.449
2ejjSAHDiphthine synthase/0.449
2jdtI5ScAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
2oh02PYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
2wf4ZY4Beta-secretase 13.4.23.460.449
3djjFADGlutathione reductase, mitochondrial1.8.1.70.449
3qx2X63Cyclin-dependent kinase 22.7.11.220.449
3toh079Gag-Pol polyprotein2.7.7.490.449
4c34STUcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
4j4nD44Peptidylprolyl isomerase/0.449
4kin1M8Mitogen-activated protein kinase 14/0.449
4mk029XBeta-adrenergic receptor kinase 12.7.11.150.449
4yzcSTUSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.449
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.449
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.448
1lf2R37Plasmepsin-23.4.23.390.448
1me6IVSPlasmepsin-23.4.23.390.448
2bt4CA23-dehydroquinate dehydratase4.2.1.100.448
2r8pT6FTransketolase 1/0.448
3c36KAIGlutamate receptor ionotropic, kainate 1/0.448
3cz7ACOHistone acetyltransferase RTT1092.3.1.480.448
3h3r14HCollagen type IV alpha-3-binding protein/0.448
3ojxFMNNADPH--cytochrome P450 reductase/0.448
3s1dZIRCytokinin dehydrogenase 11.5.99.120.448
4m83ERYOleandomycin glycosyltransferase2.4.10.448
4y3jHICEndothiapepsin3.4.23.220.448
1bwsNDPGDP-L-fucose synthase/0.447
1la2NADInositol-3-phosphate synthase5.5.1.40.447
1n2hPAJPantothenate synthetase6.3.2.10.447
1q8tY27cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
1rneC60Renin3.4.23.150.447
2a7r5GPGMP reductase 2/0.447
2c6tDT5Cyclin-dependent kinase 22.7.11.220.447
2izrBRKCasein kinase I isoform gamma-32.7.11.10.447
3w1tWRODihydroorotate dehydrogenase (fumarate)1.3.98.10.447
4lj8ADPChaperone protein ClpB/0.447
4yj2GTPTubulin alpha-1B chain/0.447
1kp2ATPArgininosuccinate synthase6.3.4.50.446
2e07SAHDiphthine synthase/0.446
2egwSAHRibosomal RNA small subunit methyltransferase E2.1.1.1930.446
2g1o2IGRenin3.4.23.150.446
3ad9NADSubunit alpha of sarocosine oxidase/0.446
3bkbSTUTyrosine-protein kinase Fes/Fps2.7.10.20.446
3fpzAHZThiamine thiazole synthase/0.446
3fwiCAMCamphor 5-monooxygenase1.14.15.10.446
3t113T1Gag-Pol polyprotein3.4.23.160.446
4l2oNADAldehyde dehydrogenase, dimeric NADP-preferring/0.446
4nwzFADFAD-dependent pyridine nucleotide-disulfide oxidoreductase/0.446
4opiFDAConserved Archaeal protein/0.446
1c3eNHRPhosphoribosylglycinamide formyltransferase/0.445
1nooCAHCamphor 5-monooxygenase1.14.15.10.445
1q8uH52cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.445
2m56CAMCamphor 5-monooxygenase1.14.15.10.445
3bheBZNGag-Pol polyprotein3.4.23.160.445
3ingNDPHomoserine dehydrogenase related protein/0.445
3kxw1ZZSaframycin Mx1 synthetase B/0.445
3vqsJT1Genome polyprotein/0.445
3w0nANPHygromycin-B 4-O-kinase2.7.1.1630.445
4burFADApoptosis-inducing factor 1, mitochondrial1.1.10.445
4dfg0JVGag-Pol polyprotein3.4.23.160.445
4iwo1H4Serine/threonine-protein kinase TBK12.7.11.10.445
1ja1FMNNADPH--cytochrome P450 reductase/0.444
1knrFADL-aspartate oxidase1.4.3.160.444
1ydtIQBcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
2b4yAPRNAD-dependent protein deacylase sirtuin-5, mitochondrial/0.444
2e8hSAHDiphthine synthase/0.444
2wf1ZY1Beta-secretase 13.4.23.460.444
3djgFADGlutathione reductase, mitochondrial1.8.1.70.444
3em3478Gag-Pol polyprotein3.4.23.160.444
3o9aK14Pol polyprotein/0.444
3q9lATPSeptum site-determining protein MinD/0.444
3s8pSAMHistone-lysine N-methyltransferase KMT5B2.1.1.430.444
3tneRITCandidapepsin-13.4.23.240.444
1f8fNADBenzyl alcohol dehydrogenase/0.443
1n2iPAJPantothenate synthetase6.3.2.10.443
1n77ATPGlutamate--tRNA ligase6.1.1.170.443
1ydrIQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
1zrzBI1Protein kinase C iota type2.7.11.130.443
2p6iSAHDiphthine synthase/0.443
2pcmSAHDiphthine synthase/0.443
2vo7M05cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
2zgzGNPPlasmid segregation protein ParM/0.443
3f03FMNPentaerythritol tetranitrate reductase/0.443
3zhyFM61-deoxy-D-xylulose 5-phosphate reductoisomerase/0.443
4a9e3PFBromodomain-containing protein 2/0.443
4ddhMS0Pantothenate synthetase6.3.2.10.443
4l4dCAMCamphor 5-monooxygenase1.14.15.10.443
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.443
1amoFMNNADPH--cytochrome P450 reductase/0.442
1k7fIAVTryptophan synthase alpha chain/0.442
1w7gMIUProthrombin3.4.21.50.442
2e8qSAHDiphthine synthase/0.442
2owuSAHDiphthine synthase/0.442
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.442
3cow52HPantothenate synthetase6.3.2.10.442
3litE15Protease/0.442
3lm9ADPPutative fructokinase2.7.1.40.442
3tvuB37Acetyl-CoA carboxylase/0.442
3vv8B02Beta-secretase 13.4.23.460.442
4ftr5HKSerine/threonine-protein kinase Chk12.7.11.10.442
4hyvPEPPyruvate kinase 12.7.1.400.442
4n6hEJ4Delta-type opioid receptor/0.442
1l4mNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.441
1q8wM77cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
1qrpHH0Pepsin A-43.4.23.10.441
1tllFMNNitric oxide synthase, brain1.14.13.390.441
1u33LM2Pancreatic alpha-amylase/0.441
1u4dDBQActivated CDC42 kinase 1/0.441
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.441
2el0SAHDiphthine synthase/0.441
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2p9dSAHDiphthine synthase/0.441
2vbdV10Isopenicillin N synthase1.21.3.10.441
2x8iX8ISerine/threonine-protein kinase Chk12.7.11.10.441
2z54AB1Gag-Pol polyprotein3.4.23.160.441
3dzvADPHydroxyethylthiazole kinase/0.441
3ixj586Beta-secretase 13.4.23.460.441
3mt817TGlycogen phosphorylase, muscle form2.4.1.10.441
3ow3SMYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
3rsv3RSBeta-secretase 13.4.23.460.441
3wycNAPMeso-diaminopimelate D-dehydrogenase1.4.1.160.441
3zo4QWIcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
4aqc88ATyrosine-protein kinase JAK2/0.441
4f32N323-oxoacyl-[acyl-carrier-protein] synthase 2/0.441
4fv6E57Mitogen-activated protein kinase 12.7.11.240.441
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.441
1bxoPP7Penicillopepsin-13.4.23.200.440
1gthFADDihydropyrimidine dehydrogenase [NADP(+)]1.3.1.20.440
1njfADPDNA polymerase III subunit tau2.7.7.70.440
1o76CAMCamphor 5-monooxygenase1.14.15.10.440
1t88CAMCamphor 5-monooxygenase1.14.15.10.440
1wc4APCAdenylate cyclase/0.440
1wngSAHDiphthine synthase/0.440
1zgv501Prothrombin3.4.21.50.440
2bxtC2DProthrombin3.4.21.50.440
2dxxSAHDiphthine synthase/0.440
2e08SAHDiphthine synthase/0.440
2g1r3IGRenin3.4.23.150.440
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.440
2x3fAPCPantothenate synthetase/0.440
3imgBZ3Pantothenate synthetase6.3.2.10.440
3r9uFADThioredoxin reductase/0.440
3ts1TYATyrosine--tRNA ligase6.1.1.10.440
4k39SAMAnaerobic sulfatase-maturating enzyme1.8.980.440
5c8wPCGcGMP-dependent protein kinase 22.7.11.120.440