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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
3amtATPtRNA(Ile2) 2-agmatinylcytidine synthetase TiaS6.3.4.22

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3amtATPtRNA(Ile2) 2-agmatinylcytidine synthetase TiaS6.3.4.221.000
1xnjADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 12.7.1.250.511
4fj0NAP17beta-hydroxysteroid dehydrogenase/0.493
1nfrNAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.490
2hrbNAPCarbonyl reductase [NADPH] 31.1.1.1840.490
1kt8ILPBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.489
3kdb006Gag-Pol polyprotein3.4.23.160.485
1i6lTYMTryptophan--tRNA ligase6.1.1.20.484
2r8oT5XTransketolase 1/0.484
1nffNAD3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.483
4fj1NAP17beta-hydroxysteroid dehydrogenase/0.482
1g0nNDPTetrahydroxynaphthalene reductase1.1.1.2520.478
1vl8NAPOxidoreductase, short chain dehydrogenase/reductase family/0.478
2tsrUMPThymidylate synthase2.1.1.450.477
4fj2NAP17beta-hydroxysteroid dehydrogenase/0.475
2f3rG5PGuanylate kinase2.7.4.80.474
4nkeIPEFarnesyl pyrophosphate synthase2.5.1.100.474
3zgz84TLeucine--tRNA ligase/0.472
1ozvSAHRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.471
1snyNAPLD36273p/0.471
3qwfNAP17beta-hydroxysteroid dehydrogenase/0.471
1phkATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform2.7.11.190.470
3fwrADPTranscriptional repressor CcpN/0.470
4briUNPEctonucleoside triphosphate diphosphohydrolase I/0.470
2rc3NADCBS domain/0.469
4hwkNAPSepiapterin reductase1.1.1.1530.469
4iqgNAPShort-chain dehydrogenase/reductase SDR/0.469
4j7uNAPSepiapterin reductase1.1.1.1530.469
4ohxADPProtein clpf-1/0.469
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.469
5idwNAPShort-chain dehydrogenase/reductase SDR/0.469
2b4qNAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.468
3c50ADPRhodopsin kinase/0.468
2z6iFMN2-nitropropane dioxygenase/0.467
1p9wANPType II secretion system protein E/0.465
2x3fAPCPantothenate synthetase/0.465
3opxU5PSuppressor of disruption of TFIIS/0.465
3sj7NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative/0.465
4yqfGDPSeptin-9/0.465
5jlaNADPutative short-chain dehydrogenase/reductase/0.465
2y42NAD3-isopropylmalate dehydrogenase1.1.1.850.464
4is3NAD3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 21.17.98.10.464
4ttbFMNIodotyrosine deiodinase 1/0.464
4k39SAMAnaerobic sulfatase-maturating enzyme1.8.980.463
4ohwATPProtein clpf-1/0.463
1ipeNDPTropinone reductase 21.1.1.2360.462
2geuCOKPantothenate kinase2.7.1.330.462
3nizADPCdc2-like CDK2/CDC28 like protein kinase/0.462
4fl3ANPTyrosine-protein kinase SYK2.7.10.20.462
4j7xNAPSepiapterin reductase1.1.1.1530.462
5ahsCOAAcyl-CoA dehydrogenase/0.462
5cwa0GAAnthranilate synthase component 14.1.3.270.462
5kjcNAJAlcohol dehydrogenase E chain1.1.1.10.462
1n2hPAJPantothenate synthetase6.3.2.10.461
2gqtFADUDP-N-acetylenolpyruvoylglucosamine reductase/0.461
2q1l8823-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.461
3rv7RVBSalicylate synthase/0.461
4e5oUMPThymidylate synthase2.1.1.450.461
5js6NAD17-beta-hydroxysteroid dehydrogenase 141.1.10.461
5k5zANPUncharacterized protein/0.461
5kjeNAJAlcohol dehydrogenase E chain1.1.1.10.461
1hk1T44Serum albumin/0.460
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.460
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.459
4j1tNADNAD/NADP transhydrogenase alpha subunit 1/0.459
1geuFADGlutathione reductase1.8.1.70.458
1k0jFADp-hydroxybenzoate hydroxylase/0.458
3cgbCOACoenzyme A disulfide reductase/0.458
5by6UMPThymidylate synthase/0.458
4cpdNADAlcohol dehydrogenase/0.457
1hv9UD1Bifunctional protein GlmU/0.456
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.456
2djlFMNDihydroorotate dehydrogenase (fumarate)1.3.98.10.456
2nmvADPUvrABC system protein B/0.456
3r7wGNPGTP-binding protein GTR2/0.456
4z54GDPNeuronal-specific septin-3/0.456
3c3nFMNDihydroorotate dehydrogenase (fumarate)1.3.98.10.455
1dj3GDPAdenylosuccinate synthetase, chloroplastic/0.454
2r8pT6FTransketolase 1/0.454
2zsbADPPantothenate kinase2.7.1.330.454
3bwjARXcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.454
3qv1NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.454
3w2jQRODihydroorotate dehydrogenase (fumarate)1.3.98.10.454
4oi2ADPProtein clpf-1/0.454
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.453
2olrATPPhosphoenolpyruvate carboxykinase (ATP)/0.453
2zz0FADThioredoxin reductase 1, cytoplasmic1.8.1.90.453
3e8nVRADual specificity mitogen-activated protein kinase kinase 12.7.12.20.453
3lcjCOAPhosphopantetheine adenylyltransferase/0.453
3nnuEDBMitogen-activated protein kinase 14/0.453
3ntdCOAFAD-dependent pyridine nucleotide-disulphide oxidoreductase/0.453
3p19NDPPutative blue fluorescent protein/0.453
3pb3SAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.453
4aw0ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.453
1b5eDCMDeoxycytidylate 5-hydroxymethyltransferase2.1.2.80.452
1ldeNADAlcohol dehydrogenase E chain1.1.1.10.452
1lolXMPOrotidine 5'-phosphate decarboxylase4.1.1.230.452
2q46NAPUncharacterized protein At5g02240/0.452
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
4own5RGAnthranilate phosphoribosyltransferase/0.452
1jvdUD1UDP-N-acetylhexosamine pyrophosphorylase2.7.7.230.451
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.451
2eudGCQRibonucleoside-diphosphate reductase large chain 11.17.4.10.451
3v0o4GWHisto-blood group ABO system transferase/0.451
1i6kTYMTryptophan--tRNA ligase6.1.1.20.450
2dknNAI3-alpha-hydroxysteroid dehydrogenase/0.450
2h2jSFGRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.450
2ooyATP5'-AMP-activated protein kinase subunit gamma/0.450
2qlnF59Glycogen phosphorylase, muscle form2.4.1.10.450
4cr8NADN-acylmannosamine 1-dehydrogenase1.1.1.2330.450
4r4uCOAAcyl-CoA thioesterase II/0.450
4zohFADPutative oxidoreductase FAD-binding subunit/0.450
1xq6NAPUncharacterized protein At5g02240/0.449
2hekGDPUncharacterized protein/0.449
2vtsLZCCyclin-dependent kinase 22.7.11.220.449
2z95NDPGDP-mannose 4,6-dehydratase/0.449
3bu5ATPInsulin receptor2.7.10.10.449
3el4ROCGag-Pol polyprotein3.4.23.160.449
3qiyQI1Botulinum neurotoxin type A3.4.24.690.449
4fv1EK4Mitogen-activated protein kinase 12.7.11.240.449
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.449
4lrlTTPHD domain protein/0.449
4u0oMTALipoyl synthase 2/0.449
5cdgNAJAlcohol dehydrogenase E chain1.1.1.10.449
1kp3ATPArgininosuccinate synthase6.3.4.50.448
2gjnFMNNitronate monooxygenase1.13.12.160.448
2wvjTTPThymidine kinase, cytosolic2.7.1.210.448
2zxgS23Aminopeptidase N3.4.11.20.448
3cow52HPantothenate synthetase6.3.2.10.448
3dwjH4BNitric oxide synthase, inducible1.14.13.390.448
3tjzGNPADP-ribosylation factor 1/0.448
4gu94GUFocal adhesion kinase 12.7.10.20.448
1edoNAP3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic1.1.1.1000.447
1rwbNADGlucose 1-dehydrogenase1.1.1.470.447
1yidATPTryptophan--tRNA ligase 26.1.1.20.447
2omeNADC-terminal-binding protein 2/0.447
2py7ATPPhosphoenolpyruvate carboxykinase (ATP)/0.447
2q641UNGag-Pol polyprotein3.4.23.160.447
2vyxFMNDodecin/0.447
3bgxTMPThymidylate synthase/0.447
3otwCOAPhosphopantetheine adenylyltransferase/0.447
3phjDHKShikimate dehydrogenase (NADP(+))/0.447
4ix5ANPUncharacterized protein/0.447
4yusFMNFamily 3 adenylate cyclase/0.447
1pf9ADP60 kDa chaperonin/0.446
2bslFMNDihydroorotate dehydrogenase A (fumarate)1.3.98.10.446
2bsmBSMHeat shock protein HSP 90-alpha/0.446
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.446
3tscNADUncharacterized protein/0.446
3ulkNDPKetol-acid reductoisomerase (NADP(+))/0.446
3wdsNADNADH-dependent quinuclidinone reductase/0.446
4dwvNAJAlcohol dehydrogenase E chain1.1.1.10.446
4onqSFGDNA methyltransferase/0.446
5eomCTPPutative nucleotidyltransferase MAB21L1/0.446
5ig2NADShort-chain dehydrogenase/reductase SDR/0.446
1jkiNAIInositol-3-phosphate synthase5.5.1.40.445
2qo9ANPEphrin type-A receptor 32.7.10.10.445
4lcjNADC-terminal-binding protein 2/0.445
1a8g2Z4Gag-Pol polyprotein3.4.23.160.444
1g7uPEP2-dehydro-3-deoxyphosphooctonate aldolase2.5.1.550.444
1ngiANPHeat shock cognate 71 kDa protein/0.444
1noiNTZGlycogen phosphorylase, muscle form2.4.1.10.444
3af4GCPPantothenate kinase2.7.1.330.444
3oz2FADDigeranylgeranylglycerophospholipid reductase/0.444
3phcIM5Purine nucleoside phosphorylase/0.444
3r9iADPSeptum site-determining protein MinD/0.444
4b8wNAPGDP-L-fucose synthase1.1.1.2710.444
4bzqADPBifunctional enzyme CysN/CysC2.7.1.250.444
4dieC5PCytidylate kinase/0.444
5cdtNAJAlcohol dehydrogenase E chain1.1.1.10.444
7upjINUGag-Pol polyprotein3.4.23.160.444
5dhhDGWNociceptin receptor/0.444
1pxjCK2Cyclin-dependent kinase 22.7.11.220.443
1u3dFADCryptochrome-1/0.443
2anb5GPGuanylate kinase2.7.4.80.443
2bkjFMNNADPH-flavin oxidoreductase/0.443
2xpuTDCTetracycline repressor protein class D/0.443
3c4vLIPD-inositol 3-phosphate glycosyltransferase2.4.1.2500.443
3q8hAO92-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.443
3uvr06FMitogen-activated protein kinase 14/0.443
3w8rACPUridine kinase/0.443
4aqc88ATyrosine-protein kinase JAK2/0.443
4c3rACPAurora kinase A2.7.11.10.443
4dq1UMPThymidylate synthase/0.443
4eb4UMPThymidylate synthase2.1.1.450.443
4r1fADPDNA topoisomerase 2-alpha5.99.1.30.443
5d3qGDPDynamin-13.6.5.50.443
5kczNAJAlcohol dehydrogenase E chain1.1.1.10.443
1u3cFADCryptochrome-1/0.442
1vzbUMPThymidylate synthase/0.442
1w49APCNTPase P4/0.442
2phkATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform2.7.11.190.442
2qrdADP5'-AMP-activated protein kinase subunit gamma/0.442
3ms421NGlycogen phosphorylase, muscle form2.4.1.10.442
3tr05GPGuanylate kinase/0.442
3wb2YGPUncharacterized protein MJ0488/0.442
4lez1SYCyclic GMP-AMP synthase/0.442
4qxr1YEStimulator of interferon genes protein/0.442
4tm0FADKtzI/0.442
1drtPCVClavaminate synthase 11.14.11.210.441
1heuNADAlcohol dehydrogenase E chain1.1.1.10.441
1u80C5PCoenzyme A biosynthesis bifunctional protein CoaBC6.3.2.50.441
2gr1FADFerredoxin reductase/0.441
2nnqT4BFatty acid-binding protein, adipocyte/0.441
2ohxNADAlcohol dehydrogenase E chain1.1.1.10.441
2qjoNADBifunctional NMN adenylyltransferase/Nudix hydrolase2.7.7.10.441
3juoAJDPhenazine biosynthesis protein A/B/0.441
3m2rCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.441
3m2rCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.441
3ogxH1SPeptidoglycan recognition protein 1/0.441
3w0sANPHygromycin-B 4-O-kinase2.7.1.1630.441
4g1f0WGDipeptidyl peptidase 4/0.441
4oplFDAConserved Archaeal protein/0.441
1xr1ANPSerine/threonine-protein kinase pim-12.7.11.10.440
1z2nADPInositol-tetrakisphosphate 1-kinase2.7.1.1340.440
2ft9CHDFatty acid-binding protein 2, liver/0.440
2rioADPSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.440
3cw901A4-chlorobenzoyl CoA ligase/0.440
3gegNADShort-chain dehydrogenase/reductase SDR/0.440
3k5uPFQAurora kinase A2.7.11.10.440
3oq6NAJAlcohol dehydrogenase E chain1.1.1.10.440
3qttANPPantothenate synthetase/0.440
3s55NADPutative short-chain dehydrogenase/reductase/0.440
3td7FADProbable FAD-linked sulfhydryl oxidase R5961.8.3.20.440
4bfsZVSPantothenate kinase2.7.1.330.440
4dyn0MRNucleoprotein/0.440
4jxxATPGlutamine--tRNA ligase6.1.1.180.440
4qnyANPMitogen activated protein kinase, putative/0.440
4r1lADPPhenylacetate-coenzyme A ligase/0.440
4uocNCNCinA-like protein/0.440