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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
1i4lGDPRas-related C3 botulinum toxin substrate 1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1i4lGDPRas-related C3 botulinum toxin substrate 1/1.000
2ql6ADPNicotinamide riboside kinase 1/0.505
3froNHFGlgA glycogen synthase/0.500
5eomCTPPutative nucleotidyltransferase MAB21L1/0.500
3ta0ATPNitrogen regulatory protein P-II (GlnB-3)/0.497
3zp4TSAChorismate mutase AroH5.4.99.50.490
1xnjADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 12.7.1.250.487
4fl2ANPTyrosine-protein kinase SYK2.7.10.20.486
3w8rACPUridine kinase/0.485
4zohFADPutative oxidoreductase FAD-binding subunit/0.485
3tqcADPPantothenate kinase/0.483
3vglANPGlucokinase/0.483
4nkeIPEFarnesyl pyrophosphate synthase2.5.1.100.482
4hmvWUBPhenazine biosynthesis protein PhzG1.40.481
4lj9ACPChaperone protein ClpB/0.481
3e9iXAHLysine--tRNA ligase6.1.1.60.480
3e6tH4BNitric oxide synthase, inducible1.14.13.390.479
3zc3NAPFerredoxin--NADP reductase1.18.1.20.479
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.477
3uu114BAnthranilate phosphoribosyltransferase/0.477
2nodH4BNitric oxide synthase, inducible1.14.13.390.476
3cisATPUniversal stress protein Rv2623/0.476
3ivmZPRProlyl endopeptidase/0.476
1dj2GDPAdenylosuccinate synthetase, chloroplastic/0.475
4zrnUPGUDP-glucose 4-epimerase, putative/0.475
3qw4U5POrotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative/0.474
1nzwNAIAldehyde dehydrogenase, mitochondrial1.2.1.30.473
3hprAP5Adenylate kinase/0.473
4jyzATPGlutamine--tRNA ligase6.1.1.180.473
2qrdADP5'-AMP-activated protein kinase subunit gamma/0.472
4n9iPCGCatabolite expression activator/0.472
2eudGCQRibonucleoside-diphosphate reductase large chain 11.17.4.10.471
3muoZPRProlyl endopeptidase/0.471
3mvwBHZNickel-binding periplasmic protein/0.471
2wd4TBVAscorbate peroxidase/0.470
3bgxTMPThymidylate synthase/0.470
3td7FADProbable FAD-linked sulfhydryl oxidase R5961.8.3.20.470
4qak2AMRNA 2',3'-cyclic phosphodiesterase/0.470
4zo3C6LAcylhomoserine lactonase/0.470
1i44ACPInsulin receptor2.7.10.10.469
4oi2ADPProtein clpf-1/0.469
1cozCTPGlycerol-3-phosphate cytidylyltransferase2.7.7.390.468
1nyxDRFPeroxisome proliferator-activated receptor gamma/0.468
1okkGCPSignal recognition particle protein/0.468
1okkGCPSignal recognition particle receptor FtsY/0.468
1qrtATPGlutamine--tRNA ligase6.1.1.180.468
3dqrH4BNitric oxide synthase, brain1.14.13.390.468
3pfiADPHolliday junction ATP-dependent DNA helicase RuvB/0.468
1dwxH4BNitric oxide synthase, inducible1.14.13.390.467
2z08ATPUniversal stress protein family/0.467
4ocgCOAFAD-dependent pyridine nucleotide-disulphide oxidoreductase/0.467
1aj22PHDihydropteroate synthase/0.466
1orrCDPCDP-paratose 2-epimerase/0.466
1wc1TATAdenylate cyclase/0.466
2gn4UD1UDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.465
2z1mGDPGDP-mannose 4,6-dehydratase/0.464
3cokANPSerine/threonine-protein kinase PLK42.7.11.210.464
3oehANPATP synthase subunit alpha, mitochondrial/0.464
1sesAHXSerine--tRNA ligase6.1.1.110.463
2qr1ADP5'-AMP-activated protein kinase subunit gamma/0.463
3av7KYNUncharacterized protein/0.463
3e6oH4BNitric oxide synthase, inducible1.14.13.390.463
4euxH4BNitric oxide synthase, brain1.14.13.390.463
3i0aDBHNeutrophil gelatinase-associated lipocalin/0.462
5kgpACOPredicted acetyltransferase/0.462
5l3rGCPCell division protein FtsY homolog, chloroplastic/0.462
1nzdUPGDNA beta-glucosyltransferase/0.461
3pngH4BNitric oxide synthase, brain1.14.13.390.461
3r9iADPSeptum site-determining protein MinD/0.461
4dieC5PCytidylate kinase/0.461
1i6kTYMTryptophan--tRNA ligase6.1.1.20.460
1ih8APCNH(3)-dependent NAD(+) synthetase6.3.1.50.460
1rj9GCPSignal recognition particle receptor FtsY/0.460
1sb9UPGWbpP/0.460
2w02ATPAcsD/0.460
2x0rNADMalate dehydrogenase/0.460
3kmwATPIntegrin-linked protein kinase2.7.11.10.460
4dzzADPPlasmid partitioning protein ParF/0.460
4fvzH4BNitric oxide synthase, brain1.14.13.390.460
1e4yAP5Adenylate kinase/0.459
1j1cADPGlycogen synthase kinase-3 beta2.7.11.260.459
2vcmM11Isopenicillin N synthase1.21.3.10.459
3nlwH4BNitric oxide synthase, brain1.14.13.390.459
4briUNPEctonucleoside triphosphate diphosphohydrolase I/0.459
4lnkADPGlutamine synthetase6.3.1.20.459
1k2tH4BNitric oxide synthase, brain1.14.13.390.458
1zzuH4BNitric oxide synthase, brain1.14.13.390.458
2r26CMCCitrate synthase2.3.3.160.458
2xpvMIYTetracycline repressor protein class D/0.458
2yvjNAIFerredoxin reductase/0.458
2z9dFMNFMN-dependent NADH-azoreductase/0.458
3dj4UD1Bifunctional protein GlmU/0.458
3sxpNADADP-L-glycero-D-mannoheptose-6-epimerase/0.458
4a4wYFBPeroxisome proliferator-activated receptor gamma/0.458
4d1oH4BNitric oxide synthase, endothelial1.14.13.390.458
5c46GSPRas-related protein Rab-11A/0.458
1ci0FMNPyridoxamine 5'-phosphate oxidase1.4.3.50.457
1n1dC2GGlycerol-3-phosphate cytidylyltransferase2.7.7.390.457
2r2nKYNKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.457
2rl1UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.457
4riyANPReceptor tyrosine-protein kinase erbB-32.7.10.10.457
2xb5I7TTetracycline repressor protein class D/0.456
4wxlBB2Peptide deformylase/0.456
5ftcADPTPR domain protein/0.456
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.455
1rs6H4BNitric oxide synthase, brain1.14.13.390.455
2wtkANPSTE20-related kinase adapter protein alpha/0.455
3cgfJNFMitogen-activated protein kinase 102.7.11.240.455
3fc5H4BNitric oxide synthase, brain1.14.13.390.454
4brgGNPEctonucleoside triphosphate diphosphohydrolase I/0.454
4k5eH4BNitric oxide synthase, brain1.14.13.390.454
4loh1SYStimulator of interferon genes protein/0.454
4oaqNDPR-specific carbonyl reductase/0.454
4own5RGAnthranilate phosphoribosyltransferase/0.454
5a02NAPGlucose-fructose oxidoreductase/0.454
5eowFAD6-hydroxynicotinate 3-monooxygenase1.14.13.1140.454
1o00NADAldehyde dehydrogenase, mitochondrial1.2.1.30.453
1v3sATPSignaling protein/0.453
2x3jATPAcsD/0.453
3rqmH4BNitric oxide synthase, brain1.14.13.390.453
3swqEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.453
4qbfAP5Adenylate kinase/0.453
4ycoFMNtRNA-dihydrouridine(16) synthase/0.453
1eyyNAPNADP-dependent fatty aldehyde dehydrogenase1.2.1.40.452
1mmvH4BNitric oxide synthase, brain1.14.13.390.452
1p6kH4BNitric oxide synthase, brain1.14.13.390.452
1sb8UD2WbpP/0.452
1vyrFMNPentaerythritol tetranitrate reductase/0.452
2bmcMPYAurora kinase A2.7.11.10.452
3enkUPGUDP-glucose 4-epimerase/0.452
3nt6COAFAD-dependent pyridine nucleotide-disulphide oxidoreductase/0.452
3o153NMThiamine-phosphate synthase/0.452
3rqkH4BNitric oxide synthase, brain1.14.13.390.452
4egbNADdTDP-glucose 4,6-dehydratase/0.452
4jlbADPAdenylate kinase/0.452
5cnsCDPRibonucleoside-diphosphate reductase 1 subunit alpha1.17.4.10.452
1zvlH4BNitric oxide synthase, brain1.14.13.390.451
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.451
2wqeADPAurora kinase A2.7.11.10.451
2yx6ADPUncharacterized protein/0.451
3hgmATPTRAP-T-associated universal stress protein TeaD/0.451
3lgxATPD-alanine--poly(phosphoribitol) ligase subunit 1/0.451
3nszANPCasein kinase II subunit alpha2.7.11.10.451
5kf1ACOPredicted acetyltransferase/0.451
5kghACOPredicted acetyltransferase/0.451
2hx3H4BNitric oxide synthase, brain1.14.13.390.450
3h4vNAPPteridine reductase 11.5.1.330.450
3lmgANPReceptor tyrosine-protein kinase erbB-32.7.10.10.450
4luxH4BNitric oxide synthase, brain1.14.13.390.450
4ohxADPProtein clpf-1/0.450
1gtrATPGlutamine--tRNA ligase6.1.1.180.449
1hk2T44Serum albumin/0.449
1jedADPSulfate adenylyltransferase/0.449
1m0wANPGlutathione synthetase6.3.2.30.449
1qrrUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.449
1s4eADPGalactokinase/0.449
2py7ATPPhosphoenolpyruvate carboxykinase (ATP)/0.449
2z7qACPRibosomal protein S6 kinase alpha-12.7.11.10.449
3rr3FLRProstaglandin G/H synthase 21.14.99.10.449
4fr8NADAldehyde dehydrogenase, mitochondrial1.2.1.30.449
4imwH4BNitric oxide synthase, brain1.14.13.390.449
4yduADPtRNA N6-adenosine threonylcarbamoyltransferase/0.449
1ipeNDPTropinone reductase 21.1.1.2360.448
1k2uH4BNitric oxide synthase, brain1.14.13.390.448
1mf0GDPAdenylosuccinate synthetase isozyme 1/0.448
3cvuFADRE11660p/0.448
3frqERYErythromycin resistance repressor protein/0.448
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.448
3pnfH4BNitric oxide synthase, brain1.14.13.390.448
4fduIHSPutative multiple inositol polyphosphate histidine phosphatase 1/0.448
4rnwFMNNADPH dehydrogenase 11.6.99.10.448
4zm3PLPAminotransferase/0.448
5bsfNADPyrroline-5-carboxylate reductase/0.448
5kjeNAJAlcohol dehydrogenase E chain1.1.1.10.448
2gevCOKPantothenate kinase2.7.1.330.447
2lbvEB4Extracellular fatty acid-binding protein/0.447
2qtrNXXProbable nicotinate-nucleotide adenylyltransferase/0.447
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.447
3hsnH4BNitric oxide synthase, brain1.14.13.390.447
3lnmNAPVoltage-gated potassium channel subunit beta-2/0.447
3nlnH4BNitric oxide synthase, brain1.14.13.390.447
3o9pMHIPeriplasmic murein peptide-binding protein/0.447
3ub5ATPActin, cytoplasmic 1/0.447
4fj0NAP17beta-hydroxysteroid dehydrogenase/0.447
4x9mFADUncharacterized protein MG039 homolog/0.447
1bidUMPThymidylate synthase/0.446
1i7lATPSynapsin-2/0.446
1kbjFMNCytochrome b2, mitochondrial1.1.2.30.446
1q3gUDAUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.446
1r35H4BNitric oxide synthase, inducible1.14.13.390.446
2yfeYFEPeroxisome proliferator-activated receptor gamma/0.446
3crlANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.446
3ge6FMNNitroreductase/0.446
3wfjNAD2-dehydropantoate 2-reductase/0.446
4d03NAPPhenylacetone monooxygenase1.14.13.920.446
1ao0ADPAmidophosphoribosyltransferase/0.445
1o02NADAldehyde dehydrogenase, mitochondrial1.2.1.30.445
2gmvPEPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.445
2j9gADPBiotin carboxylase6.3.4.140.445
2uz3TTPThymidine kinase/0.445
3h23B54Dihydropteroate synthase/0.445
3h5nATPMccB protein/0.445
3tylH4BNitric oxide synthase, brain1.14.13.390.445
3u4cNDPNADPH-dependent reductase BacG/0.445
3upkUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.445
4egiB2JHeat shock protein HSP 90-alpha/0.445
4o0uADNAurora kinase A2.7.11.10.445
4ohwATPProtein clpf-1/0.445
4qmlANPSerine/threonine-protein kinase 242.7.11.10.445
4r43GDPPhosphoenolpyruvate carboxykinase [GTP]/0.445
1i3nUD1UDP-glucose 4-epimerase/0.444
1p6jH4BNitric oxide synthase, brain1.14.13.390.444
1rywEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.444
1y8qATPSUMO-activating enzyme subunit 26.3.20.444
2ydfIO3Serum albumin/0.444
3jt4H4BNitric oxide synthase, brain1.14.13.390.444
3jt8H4BNitric oxide synthase, brain1.14.13.390.444
3jwtH4BNitric oxide synthase, brain1.14.13.390.444
3jx3H4BNitric oxide synthase, brain1.14.13.390.444
3nizADPCdc2-like CDK2/CDC28 like protein kinase/0.444
4fj2NAP17beta-hydroxysteroid dehydrogenase/0.444
1sq5ADPPantothenate kinase2.7.1.330.443
2g6j7APNitric oxide synthase, brain1.14.13.390.443
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.443
2idxATPCob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial2.5.1.170.443
2wq6FADRE11660p/0.443
3e67H4BNitric oxide synthase, inducible1.14.13.390.443
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.443
3qwfNAP17beta-hydroxysteroid dehydrogenase/0.443
3ruhUD6UDP-N-acetylglucosamine 4-epimerase/0.443
4f07FADStyrene monooxygenase component 2/0.443
4jy2FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.443
4zgsNADPutative D-lactate dehydrogenase/0.443
5bv3M7Gm7GpppX diphosphatase3.6.1.590.443
1cw3NADAldehyde dehydrogenase, mitochondrial1.2.1.30.442
1gjvAGS[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial2.7.11.40.442
1mqeAPRMutT/nudix family protein/0.442
1u5rATPSerine/threonine-protein kinase TAO22.7.11.10.442
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.442
2acxANPG protein-coupled receptor kinase 62.7.11.160.442
3p23ADPSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.442
3zxtACPDeath-associated protein kinase 12.7.11.10.442
4lrlDGTHD domain protein/0.442
1c0aAMOAspartate--tRNA ligase/0.441
2j4kU5PUridylate kinase2.7.4.220.441
2wu1FGSGlucosamine-6-phosphate deaminase3.5.99.60.441
2wzmNA7Uncharacterized oxidoreductase MSMEG_2407/MSMEI_2346/0.441
3fsySCA2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase/0.441
3nlyH4BNitric oxide synthase, brain1.14.13.390.441
3nodH4BNitric oxide synthase, inducible1.14.13.390.441
3r8814FAnthranilate phosphoribosyltransferase/0.441
4r2lATPUniversal stress protein F/0.441
5fkoTDCTetracycline repressor protein class D/0.441
1euyQSIGlutamine--tRNA ligase6.1.1.180.440
1p9wANPType II secretion system protein E/0.440
1qjfACSIsopenicillin N synthase1.21.3.10.440
1xjqADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 12.7.1.250.440
2ft9CHDFatty acid-binding protein 2, liver/0.440
2xh9J01Uncharacterized protein/0.440
2zpaACOtRNA(Met) cytidine acetyltransferase TmcA/0.440
3k5uPFQAurora kinase A2.7.11.10.440
4i8x6P3L-lactate dehydrogenase A chain1.1.1.270.440
4j7uNAPSepiapterin reductase1.1.1.1530.440
4mkhAP5Adenylate kinase/0.440
4o671SYCyclic GMP-AMP synthase/0.440
4tmcFMNOld yellow enzyme/0.440
4to3DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.440
4uczGMPLarge structural protein/0.440