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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
1ih7GMPDNA-directed DNA polymerase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1ih7GMPDNA-directed DNA polymerase/1.000
1clqGDPDNA-directed DNA polymerase/0.648
4i9qXG4DNA-directed DNA polymerase/0.599
1waj5GPDNA-directed DNA polymerase/0.595
3cfoGMPDNA-directed DNA polymerase/0.549
3bi6396Wee1-like protein kinase2.7.10.20.504
3kozZ97D-ornithine 4,5-aminomutase subunit beta/0.503
4nv0MG77-methylguanosine phosphate-specific 5'-nucleotidase/0.502
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.497
3x025GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.496
3lpgZ78Beta-glucuronidase3.2.1.310.486
2clhF19Tryptophan synthase alpha chain/0.485
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.485
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.484
3x0a5GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.479
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.478
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.477
2bakAQZMitogen-activated protein kinase 14/0.476
4a9yAQZMitogen-activated protein kinase 14/0.476
2b82ADNClass B acid phosphatase3.1.3.20.475
4ccqNAPThioredoxin reductase/0.475
1ygkRRCPyridoxal kinase2.7.1.350.474
3kp0Z98D-ornithine 4,5-aminomutase subunit beta/0.472
4gt8ADPSensor protein VraS2.7.13.30.472
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.471
2h447CAcGMP-specific 3',5'-cyclic phosphodiesterase/0.469
4kw51W6Decaprenylphosphoryl-beta-D-ribose oxidase/0.469
1dliUDXUDP-glucose 6-dehydrogenase/0.468
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.468
3lpfZ77Beta-glucuronidase3.2.1.310.468
4lez1SYCyclic GMP-AMP synthase/0.468
4yswNAIXanthine dehydrogenase/oxidase/0.468
2c1zKMPAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.467
3b5iSAHIndole-3-acetate O-methyltransferase 1/0.467
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.467
4imfSI3N-acetylneuraminate lyase/0.467
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.466
3itzP66Mitogen-activated protein kinase 14/0.466
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.466
1s3uTQDDihydrofolate reductase1.5.1.30.465
1xmmM7Gm7GpppX diphosphatase3.6.1.590.464
2in6839Wee1-like protein kinase2.7.10.20.464
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.464
3o57ZG2cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.464
3v0o4GWHisto-blood group ABO system transferase/0.464
4heu15JcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.464
1oc1ASVIsopenicillin N synthase1.21.3.10.463
3fhxPXLPyridoxal kinase2.7.1.350.463
3ppkFNISerine/threonine-protein kinase B-raf2.7.11.10.463
4hni16WCasein kinase I isoform epsilon2.7.11.10.463
4s1iPLPPyridoxal kinase, putative/0.463
2qmzLDPRibosyldihydronicotinamide dehydrogenase [quinone]/0.462
3to3ATPPetrobactin biosynthesis protein AsbB/0.462
7catNDPCatalase1.11.1.60.462
4fcd0T6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.461
1x8b824Wee1-like protein kinase2.7.10.20.460
2oc4IMHPurine nucleoside phosphorylase2.4.2.10.460
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.460
2vatCOAAcetyl-CoA--deacetylcephalosporin C acetyltransferase2.3.1.1750.460
2vbpVB1Isopenicillin N synthase1.21.3.10.460
4i9z5BAcGMP-specific 3',5'-cyclic phosphodiesterase/0.460
4ivqI43Thymidine kinase/0.460
4khnXG4DNA-directed DNA polymerase/0.460
1ra2FOLDihydrofolate reductase1.5.1.30.459
3bjcWANcGMP-specific 3',5'-cyclic phosphodiesterase/0.459
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.459
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.459
4nwiCTN7-methylguanosine phosphate-specific 5'-nucleotidase/0.459
3pqbVGPPutative oxidoreductase/0.458
4gllNADUDP-glucuronic acid decarboxylase 14.1.1.350.458
4h1e10JBeta-secretase 13.4.23.460.458
1dr3HBIDihydrofolate reductase1.5.1.30.457
2e94364Geranylgeranyl pyrophosphate synthase/0.457
3a1l2CCCytochrome P450/0.457
3cr0809Wee1-like protein kinase2.7.10.20.457
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
3fr4F8AFatty acid-binding protein, adipocyte/0.457
3o56ZG1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.457
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.457
4x5fFOLDihydrofolate reductase1.5.1.30.457
5k2bZMAAdenosine receptor A2a/0.457
2v8pCDP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.456
2w9hTOPDihydrofolate reductase1.5.1.30.456
2zjwREFCasein kinase II subunit alpha2.7.11.10.456
3o9pMHIPeriplasmic murein peptide-binding protein/0.456
3tfjTHGDimethylsulfonioproprionate demethylase DmdA2.1.1.2690.456
4m9aFDAAcyl-CoA dehydrogenase/0.456
4rtjSFGDNA adenine methylase2.1.1.720.456
1jpaANPEphrin type-B receptor 22.7.10.10.455
1yhjR6CPyridoxal kinase2.7.1.350.455
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3bgrT27Gag-Pol polyprotein2.7.7.490.455
3n10CMPAdenylate cyclase 2/0.455
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.455
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.454
2zevIPEGeranylgeranyl pyrophosphate synthase/0.454
3jqgAX6Pteridine reductase, putative/0.454
3sc13S13-phosphoinositide-dependent protein kinase 12.7.11.10.454
3v0m5GWHisto-blood group ABO system transferase/0.454
4fevPP1Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.454
1bzfTMQDihydrofolate reductase1.5.1.30.453
2oalFADFlavin-dependent tryptophan halogenase RebH1.14.19.90.453
2owb626Serine/threonine-protein kinase PLK12.7.11.210.453
3nmpPYVAbscisic acid receptor PYL2/0.453
3ntdFADFAD-dependent pyridine nucleotide-disulphide oxidoreductase/0.453
3zkuHCVIsopenicillin N synthase1.21.3.10.453
4a87NARMajor pollen allergen Bet v 1-A/0.453
1dljUGAUDP-glucose 6-dehydrogenase/0.452
1fxfMJIPhospholipase A2, major isoenzyme3.1.1.40.452
1kmyBPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.452
1rp4FADEndoplasmic oxidoreductin-11.8.40.452
2h42VIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.452
2jgbMGTEukaryotic translation initiation factor 4E type 2/0.452
2qtrNXXProbable nicotinate-nucleotide adenylyltransferase/0.452
2z3uCRRCytochrome P450/0.452
3eon341Glutaryl-CoA dehydrogenase/0.452
3q3cNADNAD-dependent L-serine dehydrogenase/0.452
4ajwVWNPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform2.7.1.1530.452
4kc1WS1Histo-blood group ABO system transferase/0.452
4n6hEJ4Delta-type opioid receptor/0.452
1k4gAIQQueuine tRNA-ribosyltransferase2.4.2.290.451
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.451
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.451
3ntaFADFAD-dependent pyridine nucleotide-disulphide oxidoreductase/0.451
4kz01UJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
4lgaA2OAbscisic acid receptor PYL2/0.451
4u0mGTPCyclic GMP-AMP synthase/0.451
4zasTYDCalS13/0.451
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.450
2g8yNADHydroxycarboxylate dehydrogenase B/0.450
2j9lATPH(+)/Cl(-) exchange transporter 5/0.450
2qtaTDPPyruvate dehydrogenase E1 component1.2.4.10.450
2v59LZKBiotin carboxylase6.3.4.140.450
3rl45GPMetallophosphoesterase MPPED23.10.450
3x0c5GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.450
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
4wzyATPMaltokinase2.7.1.1750.450
1ao8MTXDihydrofolate reductase1.5.1.30.449
1e2nRCAThymidine kinase/0.449
1ve3SAMUncharacterized protein/0.449
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
2iyiFMNAppA, antirepressor of ppsR, sensor of blue light/0.449
2vd0D27Hematopoietic prostaglandin D synthase/0.449
3q2jCKIAminoglycoside 3'-phosphotransferase2.7.1.950.449
3zkyWT4Isopenicillin N synthase1.21.3.10.449
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.449
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
3aiqHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic3.2.1.1820.448
3c35KAIGlutamate receptor ionotropic, kainate 1/0.448
3v94WYQPhosphodiesterase/0.448
3zdfNADGlyceraldehyde-3-phosphate dehydrogenase/0.448
4gh30EVQueuine tRNA-ribosyltransferase2.4.2.290.448
8catNDPCatalase1.11.1.60.448
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
2z1wBDIQueuine tRNA-ribosyltransferase2.4.2.290.447
3mesPT3Putative choline kinase/0.447
3mflDHYProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.447
3mflDHYProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.447
3n0yAPCAdenylate cyclase 2/0.447
3oafOAGDihydrofolate reductase1.5.1.30.447
4k97ATPCyclic GMP-AMP synthase/0.447
4l23X6KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform/0.447
4mt92D6Tankyrase-12.4.2.300.447
1e2jTHMThymidine kinase/0.446
1hk4T44Serum albumin/0.446
2v1aFMNNPH1-1/0.446
2v58LZJBiotin carboxylase6.3.4.140.446
2webPP4Penicillopepsin-13.4.23.200.446
2zi53L1Deoxycytidine kinase2.7.1.740.446
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
4m52FADDihydrolipoyl dehydrogenase1.8.1.40.446
4yusFMNFamily 3 adenylate cyclase/0.446
1odjGMPPurine nucleoside phosphorylase/0.445
2vbdV10Isopenicillin N synthase1.21.3.10.445
2w6zL21Biotin carboxylase6.3.4.140.445
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.445
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
4bdrKAIGlutamate receptor ionotropic, kainate 2/0.445
4wctFADFructosyl amine:oxygen oxidoreductase/0.445
3qakUKAAdenosine receptor A2a/0.445
1ay0TPPTransketolase 12.2.1.10.444
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.10.444
2xlrFADPutative flavin-containing monooxygenase/0.444
3d5wADPSerine/threonine-protein kinase PLK/0.444
4rqkATP3-phosphoinositide-dependent protein kinase 12.7.11.10.444
5e8wSTUTGF-beta receptor type-12.7.11.300.444
5kbwRBFRiboflavin transporter RibU/0.444
1dg5TOPDihydrofolate reductase1.5.1.30.443
1njjORXOrnithine decarboxylase/0.443
2o8h227cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
2v2qNVG4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.443
2y6fM9FIsopenicillin N synthase1.21.3.10.443
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3jziJZLBiotin carboxylase6.3.4.140.443
3lfzADPUncharacterized protein MJ1225/0.443
3pce3HPProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.443
3pce3HPProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.443
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
4g8cC6LAlpha/beta hydrolase fold protein/0.443
4jbxSK7Thymidine kinase/0.443
4uofDATNucleoside diphosphate kinase/0.443
5uviZMAAdenosine receptor A2a/0.443
1oj4CDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.442
1pagFMPAntiviral protein I3.2.2.220.442
1qcfPP1Tyrosine-protein kinase HCK2.7.10.20.442
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
2amb17HAndrogen receptor/0.442
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3tneRITCandidapepsin-13.4.23.240.442
3tp0FO5HTH-type transcriptional regulator EthR/0.442
3u8dU8DPhospholipase A2, membrane associated/0.442
4aw0ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.442
5c8d5ADProbable transcriptional regulator/0.442
3sn6P0GBeta-2 adrenergic receptor/0.442
1knpFADL-aspartate oxidase1.4.3.160.441
1rkpIBMcGMP-specific 3',5'-cyclic phosphodiesterase/0.441
1ro6ROLcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.441
1zapA70Candidapepsin-23.4.23.240.441
1zydATPeIF-2-alpha kinase GCN2/0.441
2iviACWIsopenicillin N synthase1.21.3.10.441
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3fu83DMLaccase-11.10.3.20.441
3phiNDPShikimate dehydrogenase (NADP(+))/0.441
3uk6ADPRuvB-like 23.6.4.120.441
3vmmP0DAlanine--anticapsin ligase/0.441
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4ej1FOLDihydrofolate reductase1.5.1.30.441
4h3g10QBeta-secretase 13.4.23.460.441
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.441
5f54TMPSingle-stranded-DNA-specific exonuclease/0.441
5hq8SAHHistone-lysine N-methyltransferase SMYD32.1.1.430.441
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
1oonFMNOxygen-insensitive NAD(P)H nitroreductase/0.440
1p33MTXPteridine reductase 11.5.1.330.440
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.440
1zisINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
2a0yDIHPurine nucleoside phosphorylase2.4.2.10.440
2brbPFQSerine/threonine-protein kinase Chk12.7.11.10.440
2dvoITTdITP/XTP pyrophosphatase3.6.1.190.440
2ovyPFJcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
2parTMP5'-deoxynucleotidase YfbR/0.440
2xvu9DNSerum albumin/0.440
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.440
3djlFADPutative acyl-CoA dehydrogenase AidB1.3.990.440
3k1wBFXRenin3.4.23.150.440
3pre3REPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
3qppPFWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
3tvxPNXcAMP-specific 3',5'-cyclic phosphodiesterase 4A3.1.4.530.440
3wtkTH4Acetylcholine-binding protein/0.440
3zdu38RCyclin-dependent kinase-like 32.7.11.220.440
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4da6GA2Purine nucleoside phosphorylase DeoD-type2.4.2.10.440
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.440
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.440