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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
5dacAGSUncharacterized protein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
5dacAGSUncharacterized protein/1.000
5da9AGSUncharacterized protein/0.575
2oapANPType II secretion system protein (GspE-2)/0.485
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.485
2ydxNAPMethionine adenosyltransferase 2 subunit beta/0.481
1cbqRE9Cellular retinoic acid-binding protein 2/0.480
4h8nNDPNADPH-dependent conjugated polyketone reductase C2/0.478
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.476
4iqgNAPShort-chain dehydrogenase/reductase SDR/0.476
1psdNADD-3-phosphoglycerate dehydrogenase1.1.1.950.474
2yvwEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.474
1cbrREACellular retinoic acid-binding protein 1/0.472
1zeoC01Peroxisome proliferator-activated receptor gamma/0.470
2j5xGSPADP-ribosylation factor 6/0.469
1rdt570Peroxisome proliferator-activated receptor gamma/0.468
2eq6FADDihydrolipoyl dehydrogenase/0.468
3fhyATPPyridoxal kinase2.7.1.350.465
4l4xNDPAmphI/0.464
4nxwADPMitochondrial dynamics protein MID51/0.464
1j21ATPArgininosuccinate synthase/0.462
1me6IVSPlasmepsin-23.4.23.390.462
3cwkREACellular retinoic acid-binding protein 2/0.462
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.461
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.461
4jin1L7RIO-type serine/threonine-protein kinase Rio12.7.11.10.461
5cnsCDPRibonucleoside-diphosphate reductase 1 subunit alpha1.17.4.10.460
2hwrDRDPeroxisome proliferator-activated receptor gamma/0.459
1u54ACPActivated CDC42 kinase 1/0.458
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.458
2yxuATPPyridoxal kinase2.7.1.350.458
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.458
4h4zFADBiphenyl dioxygenase ferredoxin reductase subunit/0.458
4kb81QOCasein kinase I isoform delta2.7.11.10.458
3qlsNDPDihydrofolate reductase1.5.1.30.457
3ukoNADAlcohol dehydrogenase class-3/0.456
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.455
3l0lHC3Nuclear receptor ROR-gamma/0.455
3wecAUICytochrome P450/0.455
4en4ATPPyridoxal kinase2.7.1.350.455
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.454
1yb5NAPQuinone oxidoreductase1.6.5.50.454
1yreCOAUncharacterized protein/0.454
3kgaLX9MAP kinase-activated protein kinase 22.7.11.10.454
1h74AGSHomoserine kinase2.7.1.390.453
3d84NDPDihydrofolate reductase1.5.1.30.453
3zuyTCHTransporter/0.453
2vnjFADNADPH:ferredoxin reductase/0.452
2w2lNADD-mandelate dehydrogenase/0.452
3cbsR12Cellular retinoic acid-binding protein 2/0.452
3gbk2PQPeroxisome proliferator-activated receptor gamma/0.452
3v9v21LPeroxisome proliferator-activated receptor gamma/0.452
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA23.6.30.452
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA1/0.452
5eypLOCTubulin beta chain/0.452
1fm9570Peroxisome proliferator-activated receptor gamma/0.451
2dwbANPAurora kinase A2.7.11.10.451
1aj8COACitrate synthase/0.450
4fg8ATPCalcium/calmodulin-dependent protein kinase type 12.7.11.170.450
1korANPArgininosuccinate synthase/0.449
1z7eATPBifunctional polymyxin resistance protein ArnA/0.449
2bx8AZQSerum albumin/0.449
2q5p241Peroxisome proliferator-activated receptor gamma/0.449
3qwfNAP17beta-hydroxysteroid dehydrogenase/0.449
3v9y24LPeroxisome proliferator-activated receptor gamma/0.449
4m4922YL-lactate dehydrogenase A chain1.1.1.270.449
4oplFDAConserved Archaeal protein/0.449
1eh4IC1Casein kinase I homolog 12.7.11.10.448
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.448
1kh2ATPArgininosuccinate synthase/0.448
1pyxANPGlycogen synthase kinase-3 beta2.7.11.260.448
2ath3EAPeroxisome proliferator-activated receptor gamma/0.448
3gwfFADCyclohexanone monooxygenase/0.448
3qlrNDPDihydrofolate reductase1.5.1.30.448
1pdhFASp-hydroxybenzoate hydroxylase/0.447
2i4zDRHPeroxisome proliferator-activated receptor gamma/0.447
2xw7NDPDihydrofolate reductase/0.447
2yvfNADFerredoxin reductase/0.447
2yvjNAIFerredoxin reductase/0.447
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
3vx4ATPPutative ABC transporter, ATP-binding protein ComA/0.447
4e5kNADPhosphonate dehydrogenase1.20.1.10.447
3zhsTD6Multifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.446
4dreNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
1zk7FADMercuric reductase1.16.1.10.445
2cbrA80Cellular retinoic acid-binding protein 1/0.445
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
2rcyNAPPyrroline-5-carboxylate reductase/0.445
3oibFDAPutative acyl-CoA dehydrogenase/0.445
3t1tGDPProbable gliding protein mglA/0.445
4b4vL34Bifunctional protein FolD/0.445
4o2bLOCTubulin beta-2B chain/0.445
1i3lNADUDP-glucose 4-epimerase/0.444
1qf4RPDAdenylosuccinate synthetase/0.444
1u4dDBQActivated CDC42 kinase 1/0.444
2izrBRKCasein kinase I isoform gamma-32.7.11.10.444
2olrATPPhosphoenolpyruvate carboxykinase (ATP)/0.444
2pobGW4Peroxisome proliferator-activated receptor gamma/0.444
2prbCOAAminoglycoside 6-N-acetyltransferase type Ib11/0.444
2v3aFADRubredoxin-NAD(+) reductase1.18.1.10.444
2x3nFADProbable FAD-dependent monooxygenase/0.444
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.444
3a3gDLZLumazine protein/0.444
3da1FADGlycerol-3-phosphate dehydrogenase/0.444
4ambDUDPutative glycosyl transferase/0.444
1ia1NDPDihydrofolate reductase1.5.1.30.443
2rlcCHDCholoylglycine hydrolase3.5.1.240.443
3d2rADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.443
3gggNADPrephenate dehydrogenase/0.443
3p67FMNPentaerythritol tetranitrate reductase/0.443
3tjzGNPADP-ribosylation factor 1/0.443
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.443
4a9hTVPBromodomain-containing protein 2/0.443
4a9mP9MBromodomain-containing protein 2/0.443
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4o1bDGBNicotinamide phosphoribosyltransferase2.4.2.120.443
4ri1ACOUDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase2.3.1.2020.443
1hncGDNGlutathione S-transferase Mu 22.5.1.180.442
1os1ATPPhosphoenolpyruvate carboxykinase (ATP)/0.442
1w4aAPCNTPase P4/0.442
3cisATPUniversal stress protein Rv2623/0.442
3clyACPFibroblast growth factor receptor 2/0.442
4jbqVX6Aurora kinase A2.7.11.10.442
4lol1YEStimulator of interferon genes protein/0.442
4q1y017Gag-Pol polyprotein3.4.23.160.442
4yagNAIC alpha-dehydrogenase/0.442
1e6wNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.441
1fm6BRLPeroxisome proliferator-activated receptor gamma/0.441
1y0s331Peroxisome proliferator-activated receptor delta/0.441
2q4wFADCytokinin dehydrogenase 71.5.99.120.441
3k6l2BBPeptide deformylase3.5.1.880.441
3wmxNADNAD dependent epimerase/dehydratase/0.441
4nxvGDPMitochondrial dynamics protein MID51/0.441
4uymVOR14-alpha sterol demethylase Cyp51B/0.441
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.440
1w5tADPORC1-type DNA replication protein 2/0.440
2aqkNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
2uzwSS4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
3p74FMNPentaerythritol tetranitrate reductase/0.440
3phiNDPShikimate dehydrogenase (NADP(+))/0.440
4jwpACOGCN5-related N-acetyltransferase/0.440
4rqkATP3-phosphoinositide-dependent protein kinase 12.7.11.10.440
4tuvCPZCytochrome P450 1191.140.440
4xldBRLPeroxisome proliferator-activated receptor gamma/0.440
4yaiNAIC alpha-dehydrogenase/0.440