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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
3h98B5PGenome polyprotein2.7.7.48

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3h98B5PGenome polyprotein2.7.7.481.000
3cwj321Genome polyprotein2.7.7.480.735
3cdeN3HGenome polyprotein2.7.7.480.686
4ih71ERGenome polyprotein2.7.7.480.685
4mk728OGenome polyprotein2.7.7.480.656
3golXNDGenome polyprotein2.7.7.480.653
3h5sH5SGenome polyprotein2.7.7.480.653
3u4o08EGenome polyprotein2.7.7.480.647
3h5uH5UGenome polyprotein2.7.7.480.645
4iz02BIGenome polyprotein2.7.7.480.644
4ih61EPGenome polyprotein2.7.7.480.642
4mk828QGenome polyprotein2.7.7.480.642
3bsa1PDGenome polyprotein2.7.7.480.641
3tyvHI3Genome polyprotein2.7.7.480.640
2fvc888Polyprotein/0.639
4mka2AYGenome polyprotein2.7.7.480.638
3co93MSGenome polyprotein2.7.7.480.634
3ska053Genome polyprotein2.7.7.480.632
3uph0C1Genome polyprotein2.7.7.480.625
3upi0C2Genome polyprotein2.7.7.480.625
1z4uPH9Polyprotein/0.621
3d5m4MSGenome polyprotein2.7.7.480.621
2gc8885Polyprotein/0.614
4eaw0NQGenome polyprotein2.7.7.480.613
3csoXNIGenome polyprotein2.7.7.480.606
3gynB42Genome polyprotein2.7.7.480.606
3cvkN34Genome polyprotein2.7.7.480.605
3d28B34Genome polyprotein2.7.7.480.593
3e51N35Genome polyprotein2.7.7.480.592
3gnwXNCGenome polyprotein2.7.7.480.582
3h59H59Genome polyprotein2.7.7.480.581
2yoj8Y6Genome polyprotein2.7.7.480.578
3gnvXNZGenome polyprotein2.7.7.480.561
1yvfPH7Polyprotein/0.550
3ske054Genome polyprotein2.7.7.480.550
2qe5617Polyprotein/0.544
4k38SAMAnaerobic sulfatase-maturating enzyme1.8.980.494
1x27ASP_TYR_VAL_HIS_PTRTyrosine-protein kinase Lck2.7.10.20.488
3juqAJDPhenazine biosynthesis protein A/B/0.483
1tehNADAlcohol dehydrogenase class-31.1.1.10.479
2x96RX3Angiotensin-converting enzyme3.4.15.10.479
1fcbFMNCytochrome b2, mitochondrial1.1.2.30.477
1u1gBBBUridine phosphorylase2.4.2.30.477
2oapANPType II secretion system protein (GspE-2)/0.476
4j0v1H7Beta-secretase 13.4.23.460.475
2c20NADUDP-glucose 4-epimerase/0.474
3b9lAZZSerum albumin/0.474
1udaUFGUDP-glucose 4-epimerase5.1.3.20.473
3udq09EBeta-secretase 13.4.23.460.473
1n2jPAFPantothenate synthetase6.3.2.10.472
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.472
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.470
2il2LIXRenin3.4.23.150.470
2ok7FADFerredoxin--NADP reductase, apicoplast/0.469
1u59STUTyrosine-protein kinase ZAP-702.7.10.20.468
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.468
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.467
1lnmDTXBilin-binding protein/0.466
1xe55FEPlasmepsin-23.4.23.390.466
4briUNPEctonucleoside triphosphate diphosphohydrolase I/0.466
1kqbFMNOxygen-insensitive NAD(P)H nitroreductase/0.465
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.464
2r8pT6FTransketolase 1/0.464
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.464
3ukfGDUUDP-galactopyranose mutase/0.464
5cmx0G6Prothrombin3.4.21.50.464
1icuFMNOxygen-insensitive NAD(P)H nitroreductase/0.463
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.462
3jzdNADMaleylacetate reductase/0.462
3qiyQI1Botulinum neurotoxin type A3.4.24.690.462
4n3l2FNProthrombin3.4.21.50.462
4rnwFMNNADPH dehydrogenase 11.6.99.10.462
1culFOKAdenylate cyclase type 2/0.461
1culFOKAdenylate cyclase type 5/0.461
4rvgTYDD-mycarose 3-C-methyltransferase/0.461
4ba5PXGProbable aminotransferase/0.460
1a4wQWEProthrombin3.4.21.50.459
2gjlFMNNitronate monooxygenase1.13.12.160.459
2xfyACXBeta-amylase3.2.1.20.459
3r3sNADPutative oxidoreductase/0.459
1xddAAYIntegrin alpha-L/0.458
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.458
2xvv9DNSerum albumin/0.458
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.458
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3otwCOAPhosphopantetheine adenylyltransferase/0.458
3p1799PProthrombin3.4.21.50.458
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.458
5kwvANPPantothenate synthetase/0.458
1jwtBLIProthrombin3.4.21.50.457
1u1f183Uridine phosphorylase2.4.2.30.457
2g8yNADHydroxycarboxylate dehydrogenase B/0.457
2wzvFMNNitroreductase NfnB/0.457
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
3own3OWRenin3.4.23.150.457
3qw8CYS_ARG_GLY_CYS_NH2Botulinum neurotoxin type A3.4.24.690.457
4ayy9MXProthrombin3.4.21.50.457
1toiHCIAspartate aminotransferase2.6.1.10.456
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.456
3zmg6Z0Beta-secretase 13.4.23.460.456
4b68NAPL-ornithine N(5)-monooxygenase/0.456
4dyn0MRNucleoprotein/0.456
4f3gKAIGlutamate receptor 3/0.456
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.456
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.456
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.456
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.455
1x1bSAHC-20 methyltransferase/0.455
2anmCDOProthrombin3.4.21.50.455
2vprTDCTetracycline repressor protein class H/0.455
3v0p4GWHisto-blood group ABO system transferase/0.455
4fxy0W2Neurolysin, mitochondrial3.4.24.160.455
4m9aFDAAcyl-CoA dehydrogenase/0.455
4uymVOR14-alpha sterol demethylase Cyp51B/0.455
1towCRZFatty acid-binding protein, adipocyte/0.454
2f3rG5PGuanylate kinase2.7.4.80.454
4b4w9L9Bifunctional protein FolD/0.454
4df2FMNNADPH dehydrogenase/0.454
4jtrIBPAldo-keto reductase family 1 member C2/0.454
2iko7IGRenin3.4.23.150.453
2r8oT5XTransketolase 1/0.453
2w02ATPAcsD/0.453
2xvw9NRSerum albumin/0.453
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.453
4i9n1E5L-lactate dehydrogenase A chain1.1.1.270.453
4kwhNAPReductase homolog/0.453
4xzjNADPutative NAD(+)--arginine ADP-ribosyltransferase Vis2.4.2.310.453
1a72PADAlcohol dehydrogenase E chain1.1.1.10.452
1icsFMN12-oxophytodienoate reductase 11.3.1.420.452
1knrFADL-aspartate oxidase1.4.3.160.452
3fr5I4AFatty acid-binding protein, adipocyte/0.452
3p8iFMNPentaerythritol tetranitrate reductase/0.452
4xqcNADHomospermidine synthase2.5.1.440.452
3x2eNAIAdenosylhomocysteinase/0.451
4k39SAMAnaerobic sulfatase-maturating enzyme1.8.980.451
1umaIN2Prothrombin3.4.21.50.450
2admSAMModification methylase TaqI2.1.1.720.450
2g1n1IGRenin3.4.23.150.450
2hk9NAPShikimate dehydrogenase (NADP(+))/0.450
3af3GCPPantothenate kinase2.7.1.330.450
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.450
3tr05GPGuanylate kinase/0.450
4bamMM9Prothrombin3.4.21.50.450
4bj9UHBTankyrase-22.4.2.300.450
4mlp2CXCryptochrome-2/0.450
4nvk2NYPeroxidase/0.450
4qxq1YEStimulator of interferon genes protein/0.450
4xguADPPutative pachytene checkpoint protein 2/0.450
1mrqSTRAldo-keto reductase family 1 member C1/0.449
2cekN8TAcetylcholinesterase3.1.1.70.449
3nbvANPKetohexokinase/0.449
4kl1PCGPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4/0.449
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.449
4r1lADPPhenylacetate-coenzyme A ligase/0.449
1cozCTPGlycerol-3-phosphate cytidylyltransferase2.7.7.390.448
1t2cNAIL-lactate dehydrogenase1.1.1.270.448
2bktRPFRenin3.4.23.150.448
2dvlFADAcyl-CoA dehydrogenase/0.448
2emrSAHDiphthine synthase/0.448
2qe2452Polyprotein/0.448
2zf051UProthrombin3.4.21.50.448
3axkNDPRibulose bisphosphate carboxylase large chain4.1.1.390.448
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.448
3ehjACPSensor histidine kinase DesK2.7.13.30.448
4gllNADUDP-glucuronic acid decarboxylase 14.1.1.350.448
1nzq162Prothrombin3.4.21.50.447
1qx4FADNADH-cytochrome b5 reductase 31.6.2.20.447
1x1aSAMC-20 methyltransferase/0.447
2xlrFADPutative flavin-containing monooxygenase/0.447
3jv7NADSecondary alcohol dehydrogenase/0.447
3maaFKPAdenylate cyclase type 2/0.447
3maaFKPAdenylate cyclase type 5/0.447
3qwc98PProthrombin3.4.21.50.447
3s5wFADL-ornithine N(5)-monooxygenase/0.447
4a802ANMajor pollen allergen Bet v 1-A/0.447
4b4vL34Bifunctional protein FolD/0.447
4l0qNADAlcohol dehydrogenase class-3/0.447
2gv8NDPThiol-specific monooxygenase1.14.130.446
2x90EALAngiotensin-converting enzyme3.4.15.10.446
3bkkKAFAngiotensin-converting enzyme3.2.10.446
3ivmZPRProlyl endopeptidase/0.446
4b63NAPL-ornithine N(5)-monooxygenase/0.446
5dp2NAPCurF/0.446
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.445
1g1aNADdTDP-glucose 4,6-dehydratase/0.445
1nl4HFPProtein farnesyltransferase subunit beta2.5.1.580.445
1x1cSAHC-20 methyltransferase/0.445
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.445
3a0tADPSensor histidine kinase/0.445
3bl7DD1m7GpppX diphosphatase3.6.1.590.445
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3fhxPLPPyridoxal kinase2.7.1.350.445
3hdyGDUUDP-galactopyranose mutase/0.445
3t7qRB4Endothiapepsin3.4.23.220.445
4dbc3QPAspartate aminotransferase2.6.1.10.445
1dduDDUThymidylate synthase/0.444
1qpl587Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.444
2bpoNAPNADPH--cytochrome P450 reductase/0.444
2lfoGCHFatty acid-binding protein, liver/0.444
2zhq27UProthrombin3.4.21.50.444
3c3nFMNDihydroorotate dehydrogenase (fumarate)1.3.98.10.444
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.444
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.444
3fp0FP015-O-acetyltransferase/0.444
3isjA8DPantothenate synthetase6.3.2.10.444
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.444
5irnADPNucleotide binding oligomerization domain containing 2/0.444
1dr3TAPDihydrofolate reductase1.5.1.30.443
1g6kNADGlucose 1-dehydrogenase1.1.1.470.443
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.443
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.443
1p0hCOAMycothiol acetyltransferase2.3.1.1890.443
1x1dSAHC-20 methyltransferase/0.443
2broDF2Serine/threonine-protein kinase Chk12.7.11.10.443
2ea4F79Methionine aminopeptidase 2/0.443
2p5fSAHDiphthine synthase/0.443
2v3oI26Prothrombin3.4.21.50.443
2xtnGTPGTPase IMAP family member 2/0.443
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
3f3sNADLambda-crystallin homolog/0.443
3tjzGNPADP-ribosylation factor 1/0.443
4b65NDPL-ornithine N(5)-monooxygenase/0.443
4egbNADdTDP-glucose 4,6-dehydratase/0.443
4en4ATPPyridoxal kinase2.7.1.350.443
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.443
4k36SAMAnaerobic sulfatase-maturating enzyme1.8.980.443
4qxr1YEStimulator of interferon genes protein/0.443
4twrNADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase/0.443
5jjsSAHGenome polyprotein/0.443
5js6NAD17-beta-hydroxysteroid dehydrogenase 141.1.10.443
1bp6UMPThymidylate synthase/0.442
1e2nRCAThymidine kinase/0.442
1f4fTP3Thymidylate synthase/0.442
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1szgFNSCytochrome b2, mitochondrial1.1.2.30.442
1t4u81AProthrombin3.4.21.50.442
1w6hTITPlasmepsin-23.4.23.390.442
2bxqIMNSerum albumin/0.442
2dhfDZFDihydrofolate reductase1.5.1.30.442
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.442
2v3hI25Prothrombin3.4.21.50.442
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.442
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.442
3c1kT15Prothrombin3.4.21.50.442
3coy53HPantothenate synthetase6.3.2.10.442
3hl4CDCCholine-phosphate cytidylyltransferase A/0.442
3nmpPYVAbscisic acid receptor PYL2/0.442
3ogwIMNLactoperoxidase1.11.1.70.442
3pqbVGPPutative oxidoreductase/0.442
3u9eCOALmo1369 protein/0.442
3udn09BBeta-secretase 13.4.23.460.442
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.442
4hxyNDPPlm1/0.442
4jdcNADProbable pyrroline-5-carboxylate dehydrogenase RocA/0.442
4m4922YL-lactate dehydrogenase A chain1.1.1.270.442
4xr9NADCalS8/0.442
5bt9NAP3-oxoacyl-(Acyl-carrier-protein) reductase/0.442
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.441
1u71MXADihydrofolate reductase1.5.1.30.441
1xh7R96cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2hg1N5OEndoplasmin/0.441
2pksG44Prothrombin3.4.21.50.441
2yy7NADL-threonine dehydrogenase/0.441
3c27DKKProthrombin3.4.21.50.441
3c35KAIGlutamate receptor ionotropic, kainate 1/0.441
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.441
3eksCY9Actin-5C/0.441
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.441
3jynNDPQuinone oxidoreductase/0.441
3q9bB3NAcetylpolyamine amidohydrolase/0.441
4baqM4ZProthrombin3.4.21.50.441
4eepFMNPhototropin-22.7.11.10.441
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.441
4h3j10WBeta-secretase 13.4.23.460.441
4jicFMNGTN Reductase/0.441
4nauAGSPhosphopantetheine adenylyltransferase/0.441
5hs1VORLanosterol 14-alpha demethylase/0.441
1dhfFOLDihydrofolate reductase1.5.1.30.440
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.440
1qy8RDIEndoplasmin/0.440
1tj0FADBifunctional protein PutA1.5.5.20.440
1vceSAHDiphthine synthase/0.440
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.440
2wf4ZY4Beta-secretase 13.4.23.460.440
2wi5ZZ5Heat shock protein HSP 90-alpha/0.440
2zsaADPPantothenate kinase2.7.1.330.440
3c3xNAPEugenol synthase 11.1.1.3180.440
3i7vB4PAP4A hydrolase/0.440
3phiNDPShikimate dehydrogenase (NADP(+))/0.440
3qdlFMNOxygen-insensitive NADPH nitroreductase/0.440
3qtv06PProthrombin3.4.21.50.440
3vucHHERenin3.4.23.150.440
4d89BXDBeta-secretase 13.4.23.460.440
4dbzNDPPutative ketoacyl reductase1.3.10.440
4dl9NADS-(hydroxymethyl)glutathione dehydrogenase/0.440
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.440
4ewo996Beta-secretase 13.4.23.460.440
4h4xFADBiphenyl dioxygenase ferredoxin reductase subunit/0.440
4id9NADPutative UDP-glucose 4-epimerase/0.440