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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
3a4lANPL-seryl-tRNA(Sec) kinase2.7.1.164

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3a4lANPL-seryl-tRNA(Sec) kinase2.7.1.1641.000
3adcANPL-seryl-tRNA(Sec) kinase2.7.1.1640.562
4yqfGDPSeptin-9/0.542
3sfuRBVPolyprotein/0.518
4hh0FMNAppA protein/0.513
4yusFMNFamily 3 adenylate cyclase/0.504
3n6mGTPGenome polyprotein/0.496
3iocA5DPantothenate synthetase6.3.2.10.495
4z54GDPNeuronal-specific septin-3/0.494
1g41ADPATP-dependent protease ATPase subunit HslU/0.491
3l9hEMQKinesin-like protein KIF11/0.491
4n49MGTCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 12.1.1.570.490
3cl2G39Neuraminidase/0.489
1pf9ADP60 kDa chaperonin/0.488
3t54ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.488
1yrxFMNAppA protein/0.487
5k5zANPUncharacterized protein/0.486
1esqTZPHydroxyethylthiazole kinase/0.485
4ez6DG3DNA polymerase I/0.485
1kp8AGS60 kDa chaperonin/0.484
3imeBZ2Pantothenate synthetase6.3.2.10.484
4jsyGTPMetallophosphoesterase/0.483
3ekuATPActin-5C/0.482
3juqAJDPhenazine biosynthesis protein A/B/0.482
3oz2FADDigeranylgeranylglycerophospholipid reductase/0.482
4fxy0W2Neurolysin, mitochondrial3.4.24.160.482
2a5uQYTPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.480
2x3fAPCPantothenate synthetase/0.480
5cypGSPSeptin-9/0.480
3fvlBHKCarboxypeptidase A13.4.17.10.479
3isjA8DPantothenate synthetase6.3.2.10.478
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.478
4ddhMS0Pantothenate synthetase6.3.2.10.478
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.478
4o8aFADBifunctional protein PutA1.2.1.880.478
1zdfUPGGlycogenin-12.4.1.1860.477
2cjmATPCyclin-dependent kinase 22.7.11.220.477
2rc3NADCBS domain/0.477
4fvz4KJNitric oxide synthase, brain1.14.13.390.477
4h1m0YJProtein-tyrosine kinase 2-beta2.7.10.20.477
1sx4ADP60 kDa chaperonin/0.476
1ytmATPPhosphoenolpyruvate carboxykinase (ATP)/0.476
4gapFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.476
5ah5LSSLeucine--tRNA ligase/0.476
2qtcTDKPyruvate dehydrogenase E1 component1.2.4.10.475
4g3pUD1Bifunctional protein GlmU/0.475
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.475
4xvuATPATPase GET3/0.475
1zarADPRIO-type serine/threonine-protein kinase Rio22.7.11.10.474
4c04SFGProtein arginine N-methyltransferase 6/0.474
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.474
1p9wANPType II secretion system protein E/0.473
1bl6SB6Mitogen-activated protein kinase 14/0.471
3iodA6DPantothenate synthetase6.3.2.10.471
4be7ATPType I restriction enzyme EcoR124II R protein3.1.21.30.471
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.470
1nzfUPGDNA beta-glucosyltransferase/0.470
2j7t274Serine/threonine-protein kinase 102.7.11.10.470
2zdgADPD-alanine--D-alanine ligase/0.470
4gb90WRPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.470
4l23X6KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform/0.470
2e9zUTPGenome polyprotein/0.469
3rgaLSBEpoxide hydrolase LasB5.5.10.469
1h48CDI2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.468
1kh2ATPArgininosuccinate synthase/0.468
1q7gNHOHomoserine dehydrogenase1.1.1.30.468
3ea0ATPATPase, ParA family/0.468
3ex8AIFRiboflavin biosynthesis protein RibD1.1.1.1930.468
4ww0ADPATP-dependent zinc metalloprotease FtsH/0.468
1h47C5P2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.467
2c9oADPRuvB-like 13.6.4.120.467
2j2pSC2Ficolin-2/0.467
3forZNPThermolysin3.4.24.270.467
3ls8AJZPhosphatidylinositol 3-kinase catalytic subunit type 32.7.1.1370.467
1mqeAPRMutT/nudix family protein/0.466
1tj2FADBifunctional protein PutA1.5.5.20.466
2iygFMNAppA, antirepressor of ppsR, sensor of blue light/0.466
3ef5DGTProbable pyrophosphohydrolase/0.466
3eksATPActin-5C/0.466
4dpwAGSMevalonate diphosphate decarboxylase/0.466
3br9DEYGenome polyprotein2.7.7.480.465
3gfzFMNUncharacterized protein/0.465
3ivgFG5Pantothenate synthetase6.3.2.10.465
4hvb19PPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.465
4lez1SYCyclic GMP-AMP synthase/0.465
5fl3ADPPili retraction protein PilT/0.465
1r6tTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.464
3buzLARActin, alpha skeletal muscle/0.464
3h03UBPGlutamate receptor 2/0.464
3lcjCOAPhosphopantetheine adenylyltransferase/0.464
3s6aANPAdenosine monophosphate-protein transferase NmFic2.7.7.n10.463
4x7wMVIMycinamicin III 3''-O-methyltransferase2.1.1.2370.463
5l3rGCPCell division protein FtsY homolog, chloroplastic/0.463
1gsuGTXGlutathione S-transferase 22.5.1.180.462
1wc4APCAdenylate cyclase/0.462
2b8tTHMThymidine kinase/0.462
3npcB96Mitogen-activated protein kinase 92.7.11.240.462
3rykTYDdTDP-4-dehydrorhamnose 3,5-epimerase/0.462
4m2bUPGUDP-glucose pyrophosphorylase/0.462
1w7h3IPMitogen-activated protein kinase 14/0.461
4bjzFADProbable salicylate monooxygenase/0.461
4ctkSAMGenome polyprotein/0.461
1nb6UTPGenome polyprotein2.7.7.480.460
2oh02PYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.460
3ogxH1SPeptidoglycan recognition protein 1/0.460
1l2oADPMyosin heavy chain, striated muscle/0.459
1omoNADAlanine dehydrogenase/0.459
2e9uA25Serine/threonine-protein kinase Chk12.7.11.10.459
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.459
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.459
3rp8FADFAD-dependent urate hydroxylase/0.459
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.459
4bk2FADProbable salicylate monooxygenase/0.459
1dq8COA3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.458
1l8aTDPPyruvate dehydrogenase E1 component1.2.4.10.458
1nlmUD1UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase/0.458
1rejB1LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.458
3f2pS3BThermolysin3.4.24.270.458
3ffkATPActin, alpha skeletal muscle/0.458
3h23B54Dihydropteroate synthase/0.458
3mh7UNK_UNK_UNK_UNK_UNKPeriplasmic serine endoprotease DegP/0.458
4ahvZ5PGag-Pol polyprotein/0.458
4bdhWVISerine/threonine-protein kinase Chk22.7.11.10.458
1i6kTYMTryptophan--tRNA ligase6.1.1.20.457
1q3qANPThermosome subunit alpha/0.457
1rdwLARActin, alpha skeletal muscle/0.457
2hmaSAMtRNA-specific 2-thiouridylase MnmA/0.457
2iyiFMNAppA, antirepressor of ppsR, sensor of blue light/0.457
3gwuSRENa(+):neurotransmitter symporter (Snf family)/0.457
3junAJDPhenazine biosynthesis protein A/B/0.457
3w0nANPHygromycin-B 4-O-kinase2.7.1.1630.457
4b1vLABActin, alpha skeletal muscle/0.457
4g3sUD1Bifunctional protein GlmU/0.457
1ijjLARActin, alpha skeletal muscle/0.456
1j21ATPArgininosuccinate synthase/0.456
1mk1APRMutT/nudix family protein/0.456
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.456
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.456
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.456
3pcrGTPADP-ribosylation factor 6/0.456
1jdvADNPurine nucleoside phosphorylase/0.455
2ooyATP5'-AMP-activated protein kinase subunit gamma/0.455
3m1fATPActin, alpha skeletal muscle/0.455
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.455
4flh14KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.455
4s1b2BALmo1466 protein/0.455
4tx9AMZPhosphoribosyl isomerase A/0.455
1yp4ADQGlucose-1-phosphate adenylyltransferase small subunit, chloroplastic/amyloplastic2.7.7.270.454
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
2zi53L1Deoxycytidine kinase2.7.1.740.454
3afhGSUGlutamate--tRNA ligase 2/0.454
3aljFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.454
3tm0ANPAminoglycoside 3'-phosphotransferase2.7.1.950.454
5agaANPDNA polymerase theta/0.454
1nzdUPGDNA beta-glucosyltransferase/0.453
1q8wM77cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.453
1qwjNCCN-acylneuraminate cytidylyltransferase2.7.7.430.453
1uayADNOxidoreductase/0.453
2w8rADPSuccinate-semialdehyde dehydrogenase, mitochondrial1.2.1.240.453
3pb5F63Endothiapepsin3.4.23.220.453
4hn1TYDdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.453
4y45F91Endothiapepsin3.4.23.220.453
1kqnNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.452
1p4aPCPPur operon repressor/0.452
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.452
2vww7X2Ephrin type-B receptor 42.7.10.10.452
3gg0FMNUncharacterized protein/0.452
3pi0F91Endothiapepsin3.4.23.220.452
4da0GNGPurine nucleoside phosphorylase DeoD-type2.4.2.10.452
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.452
5dg3U21Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase/0.452
1l8tADPAminoglycoside 3'-phosphotransferase2.7.1.950.451
1n07FMNRiboflavin kinase2.7.1.260.451
1u3dFADCryptochrome-1/0.451
2opnSUFFarnesyl pyrophosphate synthase2.5.1.100.451
2tmn0FAThermolysin3.4.24.270.451
2v3aFADRubredoxin-NAD(+) reductase1.18.1.10.451
3e8eG98cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
3jxeTYMTryptophan--tRNA ligase/0.451
3sixGDPNodulation protein Z/0.451
3sjhLARActin, alpha skeletal muscle/0.451
4fryNADPutative signal-transduction protein with CBS domains/0.451
4fxfATPPyruvate kinase PKM2.7.1.400.451
5hg0SAMPantothenate synthetase/0.451
1nmdATPMajor actin/0.450
1svlADPLarge T antigen3.6.40.450
2ieaTDPPyruvate dehydrogenase E1 component1.2.4.10.450
2ylrNAPPhenylacetone monooxygenase1.14.13.920.450
3qttANPPantothenate synthetase/0.450
4b1uLABActin, alpha skeletal muscle/0.450
4h03LARActin, alpha skeletal muscle/0.450
1q3sADPThermosome subunit alpha/0.449
1tj1FADBifunctional protein PutA1.5.5.20.449
1u3cFADCryptochrome-1/0.449
2b53D23Cyclin-dependent kinase 22.7.11.220.449
2v1xADPATP-dependent DNA helicase Q13.6.4.120.449
3cgdFADCoenzyme A disulfide reductase/0.449
3dzvADPHydroxyethylthiazole kinase/0.449
3fmjFMJMitogen-activated protein kinase 14/0.449
3hazFADBifunctional protein PutA/0.449
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.449
3kp0Z98D-ornithine 4,5-aminomutase subunit beta/0.449
1j1zATPArgininosuccinate synthase/0.448
1j7lADPAminoglycoside 3'-phosphotransferase2.7.1.950.448
1knyAPCKanamycin nucleotidyltransferase2.7.70.448
1vrqFMNSubunit alpha of sarocosine oxidase/0.448
1vrqFMNSubunit beta of sarcosine oxidase/0.448
2q97ATPActin, alpha skeletal muscle/0.448
3a13CAPRibulose bisphosphate carboxylase/0.448
3attATPPutative aminoglycoside phosphotransferase2.7.10.448
3coz54HPantothenate synthetase6.3.2.10.448
3em3478Gag-Pol polyprotein3.4.23.160.448
3ftqGNPSeptin-2/0.448
3pb3SAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.448
4a5lNDPThioredoxin reductase/0.448
5cyoGDPSeptin-9/0.448
5fs8FADApoptosis-inducing factor 1, mitochondrial1.1.10.448
1bdbNADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase/0.447
1lolXMPOrotidine 5'-phosphate decarboxylase4.1.1.230.447
1qnfHDFDeoxyribodipyrimidine photo-lyase4.1.99.30.447
2r0cFADPutative FAD-monooxygenase/0.447
2v52LABActin, alpha skeletal muscle/0.447
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.447
3rusADPChaperonin/0.447
3s2a2NQPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
3sptUD1Bifunctional protein GlmU/0.447
3vaqADNPutative adenosine kinase/0.447
4bebATPType I restriction enzyme EcoR124II R protein3.1.21.30.447
4bgbADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases/0.447
4iwyADPRibosomal protein S6--L-glutamate ligase/0.447
4k43ADPActin, alpha skeletal muscle/0.447
3hgsFMN12-oxophytodienoate reductase 31.3.1.420.446
3q2jCKIAminoglycoside 3'-phosphotransferase2.7.1.950.446
4g3qUD1Bifunctional protein GlmU/0.446
4ihqADPConserved Archaeal protein/0.446
4yklGMPAprataxin-like protein30.446
1ftlDNQGlutamate receptor 2/0.445
1x31FMNSubunit alpha of sarocosine oxidase/0.445
1x31FMNSubunit beta of sarcosine oxidase/0.445
2cvxDGTRibonucleoside-diphosphate reductase large chain 11.17.4.10.445
2olrATPPhosphoenolpyruvate carboxykinase (ATP)/0.445
3dj4UD1Bifunctional protein GlmU/0.445
3f0gC5P2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.445
3gfyFMNUncharacterized protein/0.445
3gg1FMNUncharacterized protein/0.445
3ingNDPHomoserine dehydrogenase related protein/0.445
3t4eNADQuinate/shikimate dehydrogenase/0.445
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4f1sF1SPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4icyFADPgaE/0.445
1gx1CDP2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.444
1nm1ATPMajor actin/0.444
1noiNTZGlycogen phosphorylase, muscle form2.4.1.10.444
2bpoNAPNADPH--cytochrome P450 reductase/0.444
2jj8AZZDeoxynucleoside kinase/0.444
2ohxNADAlcohol dehydrogenase E chain1.1.1.10.444
2qs1UB1Glutamate receptor ionotropic, kainate 1/0.444
2r4fRIE3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.444
2xdoFADTetX family tetracycline inactivation enzyme/0.444
2zwvSAHProbable ribosomal RNA small subunit methyltransferase/0.444
3e8cG96cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
3kozZ97D-ornithine 4,5-aminomutase subunit beta/0.444
3r9iADPSeptum site-determining protein MinD/0.444
3smkCW714-3-3 protein sigma/0.444
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.444
4cvlACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.444
4djaFAD(6-4) photolyase/0.444
4eb7PLPCysteine desulfurase IscS 2/0.444
4h2pFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.444
4j36FADKynurenine 3-monooxygenase/0.444
4jhz1KVBeta-glucuronidase3.2.1.310.444
4nkeIPEFarnesyl pyrophosphate synthase2.5.1.100.444
4zolACPTubulin tyrosine ligase/0.444
5cwa0GAAnthranilate synthase component 14.1.3.270.444
1i6lTYMTryptophan--tRNA ligase6.1.1.20.443
1lb9DNQGlutamate receptor 2/0.443
1lcbTMPThymidylate synthase/0.443
2q0uLABActin, alpha skeletal muscle/0.443
2qtaTDPPyruvate dehydrogenase E1 component1.2.4.10.443
2xauADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP433.6.4.130.443
3bk2U5PRibonuclease J/0.443
3dm5GDPSignal recognition particle 54 kDa protein/0.443
3fx6BPXCarboxypeptidase A13.4.17.10.443
3ggj25HHypoxanthine-guanine phosphoribosyltransferase2.4.2.80.443
3nw3MU2Peptidoglycan recognition protein 1/0.443
3t4nADP5'-AMP-activated protein kinase subunit gamma/0.443
4d9wX32Thermolysin3.4.24.270.443
4h0yLARActin, alpha skeletal muscle/0.443
4z17PEPEnolase/0.443
5c1pADPD-alanine--D-alanine ligase/0.443
1j39UPGDNA beta-glucosyltransferase/0.442
1zaoATPRIO-type serine/threonine-protein kinase Rio22.7.11.10.442
1zp4FAD5,10-methylenetetrahydrofolate reductase1.5.1.200.442
2hu4G39Neuraminidase/0.442
2l1rSXKTroponin C, slow skeletal and cardiac muscles/0.442
2w0hFADTrypanothione reductase/0.442
3ruvANPChaperonin/0.442
3ua808WGlutamate receptor 2/0.442
4h2w5GPAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.442
4j31FADKynurenine 3-monooxygenase/0.442
4y57F63Endothiapepsin3.4.23.220.442
1esvLARActin, alpha skeletal muscle/0.441
1jx2ADPMyosin-2 heavy chain/0.441
2gr0ADPFerredoxin reductase/0.441
2ql6ADPNicotinamide riboside kinase 1/0.441
2r86ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase/0.441
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.441
3lm8VIBThiamine pyrophosphokinase2.7.6.20.441
3mx5UTPNucleoprotein/0.441
4a4zANPAntiviral helicase SKI23.6.4.130.441
4nkeRISFarnesyl pyrophosphate synthase2.5.1.100.441
4ug91EWNitric oxide synthase oxygenase1.14.13.1650.441
4wbbADPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
1lotATPActin, alpha skeletal muscle/0.440
1ove358Mitogen-activated protein kinase 14/0.440
1r0zATPCystic fibrosis transmembrane conductance regulator/0.440
1rp7TZDPyruvate dehydrogenase E1 component1.2.4.10.440
1tu8GTXGlutathione S-transferase 22.5.1.180.440
2y3sTIRTamL/0.440
3af0GDPPantothenate kinase2.7.1.330.440
3d8vUD1Bifunctional protein GlmU/0.440
3pmuF7LEndothiapepsin3.4.23.220.440
4h0tLARActin, alpha skeletal muscle/0.440
4qnq1XJBcl-2-like protein 1/0.440