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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
3bllBPQQueuine tRNA-ribosyltransferase2.4.2.29

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3bllBPQQueuine tRNA-ribosyltransferase2.4.2.291.000
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.709
4hshQEIQueuine tRNA-ribosyltransferase2.4.2.290.689
4gcxPRFQueuine tRNA-ribosyltransferase2.4.2.290.684
4hqvQEIQueuine tRNA-ribosyltransferase2.4.2.290.675
1f3eDPZQueuine tRNA-ribosyltransferase2.4.2.290.633
4h7zGUNQueuine tRNA-ribosyltransferase2.4.2.290.630
4hvxQEIQueuine tRNA-ribosyltransferase2.4.2.290.629
1ozqPRFQueuine tRNA-ribosyltransferase2.4.2.290.626
1k4gAIQQueuine tRNA-ribosyltransferase2.4.2.290.609
3bldPRFQueuine tRNA-ribosyltransferase2.4.2.290.600
1efzPRFQueuine tRNA-ribosyltransferase2.4.2.290.565
2qzrS79Queuine tRNA-ribosyltransferase2.4.2.290.544
2z1wBDIQueuine tRNA-ribosyltransferase2.4.2.290.538
4gg90WWQueuine tRNA-ribosyltransferase2.4.2.290.537
1k4hAPQQueuine tRNA-ribosyltransferase2.4.2.290.532
4gh30EVQueuine tRNA-ribosyltransferase2.4.2.290.520
1pxgPRFQueuine tRNA-ribosyltransferase2.4.2.290.512
2bbf344Queuine tRNA-ribosyltransferase2.4.2.290.511
1q65BHBQueuine tRNA-ribosyltransferase2.4.2.290.506
3arvSAUChitinase A/0.504
1q63AIQQueuine tRNA-ribosyltransferase2.4.2.290.501
1x8b824Wee1-like protein kinase2.7.10.20.499
4bgbADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases/0.498
2xk730ESerine/threonine-protein kinase Nek22.7.11.10.497
4fps0UXQueuine tRNA-ribosyltransferase2.4.2.290.495
2cleF6FTryptophan synthase alpha chain/0.491
3s7a684Dihydrofolate reductase1.5.1.30.488
4gi40EXQueuine tRNA-ribosyltransferase2.4.2.290.484
4gh10WXQueuine tRNA-ribosyltransferase2.4.2.290.483
3sm0AEKQueuine tRNA-ribosyltransferase2.4.2.290.481
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.479
1q4wDQUQueuine tRNA-ribosyltransferase2.4.2.290.477
2z2w770Wee1-like protein kinase2.7.10.20.477
1o5rFR9Adenosine deaminase3.5.4.40.475
4kbn25UDihydrofolate reductase1.5.1.30.474
4twnB96Ephrin type-A receptor 32.7.10.10.474
1w7h3IPMitogen-activated protein kinase 14/0.471
1zdwFLVPrenyltransferase/0.470
2e99B08Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.470
4kfj1R0Dihydrofolate reductase1.5.1.30.470
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.470
2obxINI6,7-dimethyl-8-ribityllumazine synthase 22.5.1.780.469
2xk4OL2Serine/threonine-protein kinase Nek22.7.11.10.469
3rviRVIBeta-secretase 13.4.23.460.469
1pd8CO4Dihydrofolate reductase1.5.1.30.468
3biz61EWee1-like protein kinase2.7.10.20.468
3gcq1BUMitogen-activated protein kinase 14/0.468
4kebFOLDihydrofolate reductase1.5.1.30.467
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.466
1s3uTQDDihydrofolate reductase1.5.1.30.466
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.466
4fsa0V3Queuine tRNA-ribosyltransferase2.4.2.290.466
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.466
2fzjDH3Dihydrofolate reductase1.5.1.30.465
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.464
3mcyZH1FimH/0.464
3q2jCKIAminoglycoside 3'-phosphotransferase2.7.1.950.464
1b9iPXG3-amino-5-hydroxybenzoate synthase4.2.1.1440.463
3ewkFADSensory box histidine kinase/response regulator/0.463
4bfxZVXPantothenate kinase2.7.1.330.463
4kak06UDihydrofolate reductase1.5.1.30.463
1dyhDZFDihydrofolate reductase1.5.1.30.462
2bikBI1Serine/threonine-protein kinase pim-12.7.11.10.462
3pdqKC6Lysine-specific demethylase 4A1.14.110.462
3q3cNADNAD-dependent L-serine dehydrogenase/0.462
3vf60H6Glucokinase2.7.1.20.462
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.462
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.462
1r2jFADFkbI/0.461
2vq3NAPMetalloreductase STEAP3/0.461
2ydvNECAdenosine receptor A2a/0.461
3bi6396Wee1-like protein kinase2.7.10.20.461
3gncQQQGlutaryl-CoA dehydrogenase/0.461
3nxtD2EDihydrofolate reductase1.5.1.30.461
4h380YXDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.461
2webPP4Penicillopepsin-13.4.23.200.460
3nxrD2DDihydrofolate reductase1.5.1.30.460
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.460
3d4bDZDNAD-dependent protein deacetylase/0.459
3dntATPSerine/threonine-protein kinase toxin HipA/0.459
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.459
1e7vLY2Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.458
3b7dCNIGlutamate receptor 2/0.458
3dgeADPSensor histidine kinase/0.458
3pmy41LEndothiapepsin3.4.23.220.458
4eh8IRGMitogen-activated protein kinase 14/0.458
2a9z26AAdenosine kinase2.7.1.200.457
2bn4FMNNADPH--cytochrome P450 reductase/0.457
3hz6ADPXylulokinase/0.457
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.457
4f3gKAIGlutamate receptor 3/0.457
4friDWABeta-secretase 13.4.23.460.457
1ygkRRCPyridoxal kinase2.7.1.350.456
2braFAD[F-actin]-methionine sulfoxide oxidase MICAL11.14.130.456
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
2eglSAHDiphthine synthase/0.456
3dejRXCCaspase-33.4.22.560.456
4dju0KKBeta-secretase 13.4.23.460.456
4l23X6KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform/0.456
1fgiSU1Fibroblast growth factor receptor 1/0.455
1m9k7NINitric oxide synthase, endothelial1.14.13.390.455
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.455
2i4vDJRV-1 protease/0.455
2w3aTOPDihydrofolate reductase1.5.1.30.455
4biwANPSensor histidine kinase CpxA/0.455
1dr4HBIDihydrofolate reductase1.5.1.30.454
2ejzSAHDiphthine synthase/0.454
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
4iilRBFMembrane lipoprotein TpN38(b)/0.454
4ocvANPAminoglycoside phosphotransferase/0.454
4z87GDPInosine-5'-monophosphate dehydrogenase/0.454
1h65GDPTranslocase of chloroplast 343.6.50.453
1t13INI6,7-dimethyl-8-ribityllumazine synthase 2/0.453
2yisI46Mitogen-activated protein kinase 14/0.453
3qofGDPAtlastin-13.6.50.453
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.453
4ockANPN-acetylhexosamine 1-kinase2.7.1.1620.453
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.453
4y380A9Endothiapepsin3.4.23.220.453
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.452
1g7vPAI2-dehydro-3-deoxyphosphooctonate aldolase2.5.1.550.452
1ry0PG2Aldo-keto reductase family 1 member C3/0.452
1w19T1P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.452
2uxhQUEHTH-type transcriptional regulator TtgR/0.452
3ge7AFQQueuine tRNA-ribosyltransferase2.4.2.290.452
4b6l9ZPSerine/threonine-protein kinase PLK32.7.11.210.452
4gki0JNAminoglycoside 3'-phosphotransferase AphA1-IAB/0.452
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.452
4z9rNADOmega-3 polyunsaturated fatty acid synthase subunit PfaD/0.452
1e1lNAPNADPH:adrenodoxin oxidoreductase, mitochondrial1.18.1.60.451
1vceSAHDiphthine synthase/0.451
2r4tADPGlycogen synthase2.4.1.210.451
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.10.451
3jqgAX6Pteridine reductase, putative/0.451
4bftZVTPantothenate kinase2.7.1.330.451
4h3j10WBeta-secretase 13.4.23.460.451
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.451
1p0ePRFQueuine tRNA-ribosyltransferase2.4.2.290.450
2clfF6FTryptophan synthase alpha chain/0.450
2xkc4VQSerine/threonine-protein kinase Nek22.7.11.10.450
3jziJZLBiotin carboxylase6.3.4.140.450
3ue6FMNAureochrome1/0.450
3x065GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.450
1nzyBCA4-chlorobenzoyl coenzyme A dehalogenase3.8.1.70.449
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.449
2e08SAHDiphthine synthase/0.449
2egbSAHDiphthine synthase/0.449
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3rm8RM8Acidic mammalian chitinase3.2.1.140.449
4giy0WYQueuine tRNA-ribosyltransferase2.4.2.290.449
4u7wNDPMxaA/0.449
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.449
5j60FADThioredoxin reductase/0.449
1lbbKAIGlutamate receptor 2/0.448
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
2rkuR78Serine/threonine-protein kinase PLK12.7.11.210.448
2z1xPRFQueuine tRNA-ribosyltransferase2.4.2.290.448
3lfzADPUncharacterized protein MJ1225/0.448
3upkUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.448
3znsNU7Histone deacetylase 73.5.1.980.448
3zsh469Mitogen-activated protein kinase 14/0.448
4eoi1ROCyclin-dependent kinase 22.7.11.220.448
4ibmIR1Insulin receptor2.7.10.10.448
4ndnSAMS-adenosylmethionine synthase isoform type-22.5.1.60.448
2c4cFAD[F-actin]-methionine sulfoxide oxidase MICAL11.14.130.447
2ea2F77Methionine aminopeptidase 2/0.447
2eeqSAHDiphthine synthase/0.447
3adaNADSubunit alpha of sarocosine oxidase/0.447
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.447
3roeTHMNAD(P)H-hydrate epimerase5.1.99.60.447
3zdfNADGlyceraldehyde-3-phosphate dehydrogenase/0.447
4da6GA2Purine nucleoside phosphorylase DeoD-type2.4.2.10.447
4fa30SLAldo-keto reductase family 1 member C3/0.447
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4py243EMethionine--tRNA ligase/0.447
1ove358Mitogen-activated protein kinase 14/0.446
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.446
2dv3SAHDiphthine synthase/0.446
2e16SAHDiphthine synthase/0.446
2h00SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase/0.446
2x06NADL-sulfolactate dehydrogenase/0.446
3c36KAIGlutamate receptor ionotropic, kainate 1/0.446
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3hv3R49Mitogen-activated protein kinase 14/0.446
3pm1ETHTH-type transcriptional regulator QacR/0.446
4appN53Serine/threonine-protein kinase PAK 42.7.11.10.446
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.446
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
1a8rGTPGTP cyclohydrolase 13.5.4.160.445
1ao8MTXDihydrofolate reductase1.5.1.30.445
1n3sGTPGTP cyclohydrolase 13.5.4.160.445
1pr4MTPPurine nucleoside phosphorylase DeoD-type/0.445
1synF89Thymidylate synthase/0.445
2b35TCLEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.445
2pcgSAHDiphthine synthase/0.445
2pkmADNAdenosine kinase2.7.1.200.445
3ihgVAKAklavinone 12-hydroxylase RdmE/0.445
3kfmKAIGlutamate receptor 4/0.445
3owxXRARibosyldihydronicotinamide dehydrogenase [quinone]/0.445
3pe2E1BCasein kinase II subunit alpha2.7.11.10.445
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4fevPP1Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.445
4li61XOTankyrase-12.4.2.300.445
1e800GQEndothiapepsin3.4.23.220.444
1fw0KAIGlutamate receptor 2/0.444
1jf2CZHObelin/0.444
1mq0BRDCytidine deaminase3.5.4.50.444
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.444
2in6839Wee1-like protein kinase2.7.10.20.444
3anmSYD1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.444
3eon341Glutaryl-CoA dehydrogenase/0.444
3fhxPXLPyridoxal kinase2.7.1.350.444
3ielU5PRibonuclease TTHA02523.10.444
3qv1NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.444
3zh8C58Protein kinase C iota type2.7.11.130.444
4bfvZVVPantothenate kinase2.7.1.330.444
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.444
4jlm1NNDeoxycytidine kinase2.7.1.740.444
4zz6CTPRibosome inactivating protein/0.444
5d7pOCZNAD-dependent protein deacetylase sirtuin-23.5.10.444
3d4sTIMBeta-2 adrenergic receptor/0.444
1jdzFMBPurine nucleoside phosphorylase/0.443
2cftPLPPyridoxal phosphate phosphatase/0.443
2cjfRP43-dehydroquinate dehydratase4.2.1.100.443
2egsSAHDiphthine synthase/0.443
2ejkSAHDiphthine synthase/0.443
2x7jTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.443
3o73O73Ribosyldihydronicotinamide dehydrogenase [quinone]/0.443
3rsv3RSBeta-secretase 13.4.23.460.443
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.443
4c72TLG3-oxoacyl-ACP synthase/0.443
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4h3g10QBeta-secretase 13.4.23.460.443
4v0s2HN3-dehydroquinate dehydratase4.2.1.100.443
1mvsDTMDihydrofolate reductase1.5.1.30.442
1n5vNOMActVA 6 protein/0.442
1s9qOHTEstrogen-related receptor gamma/0.442
1xddAAYIntegrin alpha-L/0.442
2gfsPQBMitogen-activated protein kinase 14/0.442
2io6330Wee1-like protein kinase2.7.10.20.442
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
3gyf51PDihydrofolate reductase1.5.1.30.442
3h3qH13Collagen type IV alpha-3-binding protein/0.442
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
5gcnCOAHAT A1/0.442
1hb1OCVIsopenicillin N synthase1.21.3.10.441
1krv147Galactoside O-acetyltransferase2.3.1.180.441
1mvtDTMDihydrofolate reductase1.5.1.30.441
2ejuSAHtRNA (guanine(26)-N(2))-dimethyltransferase/0.441
2pchSAHDiphthine synthase/0.441
2pncCLUPrimary amine oxidase, liver isozyme/0.441
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3slkNDPPolyketide synthase extender module 2/0.441
3vilSA0Beta-glucosidase/0.441
3zoiM2WIsopenicillin N synthase1.21.3.10.441
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.441
4iyg1HUStrictosidine synthase4.3.3.20.441
1kuyCOTSerotonin N-acetyltransferase/0.440
1n3rGTPGTP cyclohydrolase 13.5.4.160.440
1svgI04cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
1vjy460TGF-beta receptor type-12.7.11.300.440
1wetGUNHTH-type transcriptional repressor PurR/0.440
2pb6SAHDiphthine synthase/0.440
3h3r14HCollagen type IV alpha-3-binding protein/0.440
3l08ZIGPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
3ntaFADFAD-dependent pyridine nucleotide-disulphide oxidoreductase/0.440
3oafOAGDihydrofolate reductase1.5.1.30.440
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4eerFMNPhototropin-22.7.11.10.440
4eol1ROCyclin-dependent kinase 22.7.11.220.440
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
5auzGENDeath-associated protein kinase 12.7.11.10.440
5dp2NAPCurF/0.440
5iubCLRAdenosine receptor A2a/0.440