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

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3adcANPL-seryl-tRNA(Sec) kinase2.7.1.1641.000
3a4lANPL-seryl-tRNA(Sec) kinase2.7.1.1640.541
1nb6UTPGenome polyprotein2.7.7.480.519
4g3qUD1Bifunctional protein GlmU/0.513
4ic7ANPMitogen-activated protein kinase 72.7.11.240.513
5ayzNCNNicotinate-nucleotide pyrophosphorylase [carboxylating]2.4.2.190.505
3t54ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.504
4dpwAGSMevalonate diphosphate decarboxylase/0.497
2j7t274Serine/threonine-protein kinase 102.7.11.10.495
2opnSUFFarnesyl pyrophosphate synthase2.5.1.100.494
2q6bHR23-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.492
4be7ATPType I restriction enzyme EcoR124II R protein3.1.21.30.488
3qw4U5POrotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative/0.485
4g3pUD1Bifunctional protein GlmU/0.485
1kp8AGS60 kDa chaperonin/0.484
4ez6DG3DNA polymerase I/0.483
4g3sUD1Bifunctional protein GlmU/0.482
1pf9ADP60 kDa chaperonin/0.480
3jukUPGUTP--glucose-1-phosphate uridylyltransferase/0.480
3dmhSAMProbable ribosomal RNA small subunit methyltransferase/0.478
3l9hEMQKinesin-like protein KIF11/0.478
3tm0ANPAminoglycoside 3'-phosphotransferase2.7.1.950.478
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.478
4xjxATPType I restriction enzyme EcoR124II R protein3.1.21.30.477
2j2pSC2Ficolin-2/0.475
1n07FMNRiboflavin kinase2.7.1.260.474
1wc1TATAdenylate cyclase/0.474
3npcB96Mitogen-activated protein kinase 92.7.11.240.473
3rt4LP5Peptidoglycan recognition protein 1/0.473
1ijjLARActin, alpha skeletal muscle/0.472
4j31FADKynurenine 3-monooxygenase/0.472
5fs8FADApoptosis-inducing factor 1, mitochondrial1.1.10.472
4jsyGTPMetallophosphoesterase/0.471
2xvu9DNSerum albumin/0.470
2a5uQYTPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.469
2c4cFAD[F-actin]-methionine sulfoxide oxidase MICAL11.14.130.469
2gvgNMNNicotinamide phosphoribosyltransferase2.4.2.120.469
3juqAJDPhenazine biosynthesis protein A/B/0.469
4h2w5GPAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.469
4z17PEPEnolase/0.469
2vwpNDPGlucose 1-dehydrogenase/0.468
2wvlGDDMannosyl-3-phosphogylcerate synthase/0.468
4i9aNCNNicotinate-nucleotide pyrophosphorylase [carboxylating]/0.468
4l06NAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.468
2vr1ATFBiotin carboxylase6.3.4.140.467
2x3fAPCPantothenate synthetase/0.467
3gcuR48Mitogen-activated protein kinase 14/0.467
1ove358Mitogen-activated protein kinase 14/0.466
1wc6TATAdenylate cyclase/0.466
3hkwIX6Genome polyprotein2.7.7.480.466
3sfuRBVPolyprotein/0.466
5a65TPPThiamine-triphosphatase3.6.1.280.466
5bpfADPD-alanine--D-alanine ligase/0.466
1lj8NADMannitol dehydrogenase/0.465
3q8xUD1Toxin zeta/0.465
4jrnANPRhoptry kinase family protein/0.465
4rwtANPActin-5C/0.464
1bl6SB6Mitogen-activated protein kinase 14/0.463
2zwvSAHProbable ribosomal RNA small subunit methyltransferase/0.463
3h03UBPGlutamate receptor 2/0.463
3wdlATP4-phosphopantoate--beta-alanine ligase6.3.2.360.463
4nkeIPEFarnesyl pyrophosphate synthase2.5.1.100.463
4yhjAN2G protein-coupled receptor kinase 42.7.11.160.463
1dq9HMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.462
1g1lDAUGlucose-1-phosphate thymidylyltransferase/0.462
1n38U3HRNA-directed RNA polymerase lambda-32.7.7.480.462
2bryFAD[F-actin]-methionine sulfoxide oxidase MICAL11.14.130.462
2vo0M03cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.462
4becATPType I restriction enzyme EcoR124II R protein3.1.21.30.461
4mb2ATPUncharacterized protein/0.461
4ww0ADPATP-dependent zinc metalloprotease FtsH/0.461
2q7hYLYPyrrolysine--tRNA ligase/0.460
3dj4UD1Bifunctional protein GlmU/0.460
3ef5DGTProbable pyrophosphohydrolase/0.460
3t9aANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.460
1j21ATPArgininosuccinate synthase/0.459
1svmATPLarge T antigen3.6.40.459
3ryoACON-acetyltransferase Eis/0.459
3t99ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.459
4kzoNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.459
5c1pADPD-alanine--D-alanine ligase/0.459
1r0zATPCystic fibrosis transmembrane conductance regulator/0.458
1sx4ADP60 kDa chaperonin/0.458
3gfzFMNUncharacterized protein/0.458
4cw5FMNDfnA/0.458
4j33FADKynurenine 3-monooxygenase/0.458
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.457
5eomCTPPutative nucleotidyltransferase MAB21L1/0.457
2jjxATPUridylate kinase/0.456
2ydfIO3Serum albumin/0.456
3gg0FMNUncharacterized protein/0.456
3ogxH1SPeptidoglycan recognition protein 1/0.456
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.456
4kq1U5PGlycogen [starch] synthase/0.456
4txiFAD[F-actin]-methionine sulfoxide oxidase MICAL11.14.130.456
1tqpATPRIO-type serine/threonine-protein kinase Rio22.7.11.10.455
4yusFMNFamily 3 adenylate cyclase/0.455
1mabATPATP synthase subunit alpha, mitochondrial/0.454
3q9lATPSeptum site-determining protein MinD/0.454
4bv6FADApoptosis-inducing factor 1, mitochondrial1.1.10.454
1p4aPCPPur operon repressor/0.453
2vrx447Aurora kinase B-A2.7.11.10.453
3nw3MU2Peptidoglycan recognition protein 1/0.453
4d58BI9Focal adhesion kinase 12.7.10.20.453
4h1m0YJProtein-tyrosine kinase 2-beta2.7.10.20.453
4l455FIRibosomal protein S6 kinase beta-12.7.11.10.453
4o6nCDPUncharacterized protein/0.453
1yp4ADQGlucose-1-phosphate adenylyltransferase small subunit, chloroplastic/amyloplastic2.7.7.270.452
2qtaTDPPyruvate dehydrogenase E1 component1.2.4.10.452
2vkdUPGCytotoxin L/0.452
2wlfACOPolysialic acid O-acetyltransferase/0.452
4bebATPType I restriction enzyme EcoR124II R protein3.1.21.30.452
4bgbADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases/0.452
4cpdNADAlcohol dehydrogenase/0.452
4ev0CMPCyclic AMP receptor protein/0.452
4j36FADKynurenine 3-monooxygenase/0.452
4yswNAIXanthine dehydrogenase/oxidase/0.452
1q7gNHOHomoserine dehydrogenase1.1.1.30.451
1ytmATPPhosphoenolpyruvate carboxykinase (ATP)/0.451
3ekuATPActin-5C/0.451
3fpbCZASarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.451
4jlbADPAdenylate kinase/0.451
1w7h3IPMitogen-activated protein kinase 14/0.450
2z86UGAChondroitin synthase2.4.1.1750.450
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
1w84L12Mitogen-activated protein kinase 14/0.449
2q1l8823-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.449
2w7xD1ASerine/threonine-protein kinase Chk22.7.11.10.449
3gfyFMNUncharacterized protein/0.449
3gg1FMNUncharacterized protein/0.449
3h5nATPMccB protein/0.449
3lj3WYEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
4i3p1CW3-hydroxyanthranilate 3,4-dioxygenase/0.449
4z36ON3Lysophosphatidic acid receptor 1/0.449
1ao0ADPAmidophosphoribosyltransferase/0.448
1dq8COA3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.448
2bkkADPAminoglycoside 3'-phosphotransferase2.7.1.950.448
3epsATPIsocitrate dehydrogenase kinase/phosphatase/0.448
3pfiADPHolliday junction ATP-dependent DNA helicase RuvB/0.448
3w2o03PEpidermal growth factor receptor2.7.10.10.448
1lolXMPOrotidine 5'-phosphate decarboxylase4.1.1.230.447
2yitYITSerine/threonine-protein kinase Chk22.7.11.10.447
2zx5ZX5Alpha-L-fucosidase, putative/0.447
3pduNAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase/0.447
3t4eNADQuinate/shikimate dehydrogenase/0.447
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
4burFADApoptosis-inducing factor 1, mitochondrial1.1.10.447
4da4SAHDNA (cytosine-5)-methyltransferase 12.1.1.370.447
4flh14KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
4guvFADTetX family tetracycline inactivation enzyme/0.447
4kwwPHTNicotinate-nucleotide pyrophosphorylase [carboxylating]2.4.2.190.447
1finATPCyclin-dependent kinase 22.7.11.220.446
1g3lTRHGlucose-1-phosphate thymidylyltransferase/0.446
1q8wM77cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
1wc5APCAdenylate cyclase/0.446
2ad5ADPCTP synthase/0.446
2r4fRIE3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.446
3m1fATPActin, alpha skeletal muscle/0.446
3qyw6PBMitogen-activated protein kinase 12.7.11.240.446
4ci6ATPActin/0.446
4j2wFADKynurenine 3-monooxygenase/0.446
4jhz1KVBeta-glucuronidase3.2.1.310.446
1ftlDNQGlutamate receptor 2/0.445
2rc3NADCBS domain/0.445
3e8cG96cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.445
3n0yAPCAdenylate cyclase 2/0.445
4c04SFGProtein arginine N-methyltransferase 6/0.445
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
1kwsUGAGalactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3/0.444
3dmgSAHProbable ribosomal RNA small subunit methyltransferase/0.444
3lxdFADFAD-dependent pyridine nucleotide-disulfide oxidoreductase/0.444
4d79ATPtRNA threonylcarbamoyladenosine dehydratase6.10.444
4lnkADPGlutamine synthetase6.3.1.20.444
1n35CH1RNA-directed RNA polymerase lambda-32.7.7.480.443
3e8eG98cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
3hgmATPTRAP-T-associated universal stress protein TeaD/0.443
3supDCPDNA-directed DNA polymerase/0.443
3t9dANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.443
3vvh4BMDual specificity mitogen-activated protein kinase kinase 12.7.12.20.443
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4k6rATPBifunctional protein GlmU/0.443
1bl7SB4Mitogen-activated protein kinase 14/0.442
1gsuGTXGlutathione S-transferase 22.5.1.180.442
1h5sTMPGlucose-1-phosphate thymidylyltransferase 1/0.442
1j7uANPAminoglycoside 3'-phosphotransferase2.7.1.950.442
1mqeAPRMutT/nudix family protein/0.442
1s4pGDPGlycolipid 2-alpha-mannosyltransferase/0.442
1u3cFADCryptochrome-1/0.442
2i4mPSDProline--tRNA ligase6.1.1.150.442
2uzuL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
3t9eADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.442
4e5h0N8Polymerase acidic protein/0.442
4n49MGTCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 12.1.1.570.442
4u0oMTALipoyl synthase 2/0.442
4x4jFADPutative oxygenase/0.442
1ebuNDAHomoserine dehydrogenase1.1.1.30.441
1eqyATPActin, alpha skeletal muscle/0.441
1lb9DNQGlutamate receptor 2/0.441
1nzwNAIAldehyde dehydrogenase, mitochondrial1.2.1.30.441
3ffkATPActin, alpha skeletal muscle/0.441
3u78E67Lysine-specific demethylase 7A1.14.110.441
1w82L10Mitogen-activated protein kinase 14/0.440
3hiyUTPUncharacterized protein/0.440
3nmuSAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase/0.440
4n9wGDPPhosphatidyl-myo-inositol mannosyltransferase2.4.1.570.440
5dm3ADPL-glutamine synthetase/0.440