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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
5dkkFMNPredicted protein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
5dkkFMNPredicted protein/1.000
5djtFMNNPH1-2/0.605
4hhdFMNPhototropin-12.7.11.10.578
4eepFMNPhototropin-22.7.11.10.577
3t50FMNBlue-light-activated histidine kinase2.7.13.30.575
3ue6FMNAureochrome1/0.571
4eerFMNPhototropin-22.7.11.10.571
5djuFMNNPH1-2/0.566
2z6dFMNPhototropin-22.7.11.10.565
2pd8FADVivid PAS protein VVD/0.561
4eetFMNPhototropin-22.7.11.10.550
3is2FADVivid PAS protein VVD/0.546
1n9nFMNPutative blue light receptor/0.545
2pd7FADVivid PAS protein VVD/0.536
3hjiFADVivid PAS protein VVD/0.536
5efwFMNNPH1-1/0.536
1g28FMNPHY3/0.529
2pr5FMNBlue-light photoreceptor/0.523
2v1aFMNNPH1-1/0.523
3p7nFMNLight-activated DNA-binding protein EL222/0.523
4eeuFMNPhototropin-22.7.11.10.520
2z6cFMNPhototropin-12.7.11.10.519
2pdtFADVivid PAS protein VVD/0.517
3b9lAZZSerum albumin/0.516
3d72FADVivid PAS protein VVD/0.514
4wujFMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy/0.511
3hjkFADVivid PAS protein VVD/0.506
1n9lFMNPutative blue light receptor/0.502
3sw1FMNSensory box protein/0.502
4hj6FMNLOV protein/0.501
3u2mFADFAD-linked sulfhydryl oxidase ALR1.8.3.20.500
4fvqATPTyrosine-protein kinase JAK2/0.500
4eesFMNPhototropin-22.7.11.10.491
4hiaFMNLOV protein/0.491
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.489
2ifaFMNUncharacterized protein/0.488
2v0uFMNNPH1-1/0.486
4rpgFADUDP-galactopyranose mutase5.4.99.90.485
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.482
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.481
3ruqADPChaperonin/0.478
4blsAPCNTPase P4/0.478
4iah1DXAlr2278 protein/0.477
2xvv9DNSerum albumin/0.476
2ehqNAP1-pyrroline-5-carboxylate dehydrogenase/0.475
3f3sNADLambda-crystallin homolog/0.474
3gfbNADL-threonine 3-dehydrogenase/0.474
1kqdFMNOxygen-insensitive NAD(P)H nitroreductase/0.473
2ehuNAD1-pyrroline-5-carboxylate dehydrogenase/0.473
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.473
4kukRBFPutative blue-light photoreceptor/0.473
3t9aANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.472
4fvrATPTyrosine-protein kinase JAK2/0.472
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.470
5kghACOPredicted acetyltransferase/0.470
4do30LAFatty-acid amide hydrolase 13.5.1.990.469
1nzfUPGDNA beta-glucosyltransferase/0.467
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
1f20FADNitric oxide synthase, brain1.14.13.390.466
2xvw9NRSerum albumin/0.466
3jvhHHV2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.466
1bcpATPPertussis toxin subunit 4/0.465
1bcpATPPertussis toxin subunit 5/0.465
2bpoNAPNADPH--cytochrome P450 reductase/0.465
1oyaFMNNADPH dehydrogenase 11.6.99.10.464
1vfrFMNMajor NAD(P)H-flavin oxidoreductase1.6.990.463
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
2fvlNAPAldo-keto reductase family 1 member C41.1.1.2250.462
2j7t274Serine/threonine-protein kinase 102.7.11.10.462
3s1dZIRCytokinin dehydrogenase 11.5.99.120.462
4kgmATPUncharacterized protein/0.462
2qenADPWalker-Type ATPase/0.461
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
2bxqIMNSerum albumin/0.459
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.459
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.459
3ruhNADUDP-N-acetylglucosamine 4-epimerase/0.459
4yswFADXanthine dehydrogenase/oxidase/0.459
2j40NAD1-pyrroline-5-carboxylate dehydrogenase/0.458
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.458
3uylTYDProbable NDP-rhamnosyltransferase/0.458
4cojDTPUncharacterized protein/0.458
4q4cADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.458
1hquHBYGag-Pol polyprotein2.7.7.490.457
1j7kATPHolliday junction ATP-dependent DNA helicase RuvB/0.457
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.457
2a4zBYMPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.457
4a83DXCMajor pollen allergen Bet v 1-A/0.457
4gvjADPNon-receptor tyrosine-protein kinase TYK22.7.10.20.457
4i8x6P3L-lactate dehydrogenase A chain1.1.1.270.457
4kwhNAPReductase homolog/0.457
4r38RBFBlue-light-activated histidine kinase 22.7.13.30.457
1bxsNADRetinal dehydrogenase 11.2.1.360.456
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.456
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
4dpwAGSMevalonate diphosphate decarboxylase/0.456
2w6oOA3Biotin carboxylase6.3.4.140.455
3a4oSTUTyrosine-protein kinase Lyn2.7.10.20.455
3eem53VUncharacterized protein/0.455
3q8hAO92-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.455
4a5lNDPThioredoxin reductase/0.455
5fm6ADPRuvB-like helicase/0.455
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4dc0NDPPutative ketoacyl reductase1.3.10.454
1in5ADPHolliday junction ATP-dependent DNA helicase RuvB/0.453
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.453
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.453
3nsh957Beta-secretase 13.4.23.460.453
3zdu38RCyclin-dependent kinase-like 32.7.11.220.453
4i0i957Beta-secretase 13.4.23.460.453
5kgpACOPredicted acetyltransferase/0.453
1w06W05Isopenicillin N synthase1.21.3.10.452
1w4aAPCNTPase P4/0.452
2c5eGDDGDP-mannose 3,5-epimerase5.1.3.180.452
4hwkNAPSepiapterin reductase1.1.1.1530.452
1ipeNDPTropinone reductase 21.1.1.2360.451
3t9fADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.451
4dbzNDPPutative ketoacyl reductase1.3.10.451
4oagADPMitochondrial dynamics protein MID51/0.451
1kr2TADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.450
2aq8NAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.450
3rusADPChaperonin/0.450
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.450
4a4zANPAntiviral helicase SKI23.6.4.130.450
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.450
4jldADPAdenylate kinase/0.450
1f20NAPNitric oxide synthase, brain1.14.13.390.449
1g6oADPCag alpha/0.449
3g8dADPBiotin carboxylase6.3.4.140.449
3h3sH15Collagen type IV alpha-3-binding protein/0.449
3mnrSD1Heat shock protein HSP 90-alpha/0.449
4c57FEFCyclin-G-associated kinase2.7.11.10.449
4iae1DXAlr2278 protein/0.449
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.448
1uxjNADMalate dehydrogenase/0.448
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.448
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.448
2rhrEMOPutative ketoacyl reductase1.3.10.448
2y0mACOHistone acetyltransferase KAT8/0.448
3copADPGlycogen synthase2.4.1.210.448
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3lqfNADGalactitol dehydrogenase/0.448
3pvt3HC1,2-phenylacetyl-CoA epoxidase, subunit A1.14.13.1490.448
4gb90WRPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
4xzmNAPAldo-keto reductase family 1 member B101.1.10.448
5j3wFMNSensory box protein/0.448
5kf1ACOPredicted acetyltransferase/0.448
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.447
2c29NAPDihydroflavonol 4-reductase/0.447
2j3nNAPThioredoxin reductase 1, cytoplasmic1.8.1.90.447
3r9iADPSeptum site-determining protein MinD/0.447
4gyy12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.447
4rgqNDPGlycerol-1-phosphate dehydrogenase [NAD(P)+]/0.447
1t1sCBQ1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.446
1ykiFMNOxygen-insensitive NAD(P)H nitroreductase/0.446
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.446
2g37FADProline dehydrogenase/0.446
2gjnFMNNitronate monooxygenase1.13.12.160.446
2x0iNAIMalate dehydrogenase/0.446
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4ig01FGGag-Pol polyprotein2.7.7.490.446
4jqh1MFAlr2278 protein/0.446
1i7lATPSynapsin-2/0.445
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
2a94AP0L-lactate dehydrogenase1.1.1.270.445
2ggsNDPdTDP-4-dehydrorhamnose reductase/0.445
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
2rc6NAPFerredoxin--NADP reductase/0.445
3dd125DGlycogen phosphorylase, liver form2.4.1.10.445
3eej53RUncharacterized protein/0.445
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.445
3vhxGTPADP-ribosylation factor 6/0.445
4ft0HK9Serine/threonine-protein kinase Chk12.7.11.10.445
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4j36FADKynurenine 3-monooxygenase/0.445
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.445
4wucANPDNA gyrase subunit B/0.445
5j4eFMNSensory box protein/0.445
1g1aNADdTDP-glucose 4,6-dehydratase/0.444
1i2cUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.444
1mjbACOHistone acetyltransferase ESA1/0.444
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
1oc1ASVIsopenicillin N synthase1.21.3.10.444
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.444
1qiqACCIsopenicillin N synthase1.21.3.10.444
1t2cNAIL-lactate dehydrogenase1.1.1.270.444
2x7hPFNProstaglandin reductase 310.444
2yy7NADL-threonine dehydrogenase/0.444
3efvNADPutative succinate-semialdehyde dehydrogenase/0.444
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.444
3jynNDPQuinone oxidoreductase/0.444
3p0fBAUUridine phosphorylase 22.4.2.30.444
3w2eNADNADH-cytochrome b5 reductase 31.6.2.20.444
3w6uNAP6-phosphogluconate dehydrogenase, NAD-binding protein/0.444
4bfzZVZPantothenate kinase2.7.1.330.444
4fv3EK6Mitogen-activated protein kinase 12.7.11.240.444
4i6gFADCryptochrome-2/0.444
4xdmGDMHeat shock cognate 90 kDa protein/0.444
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.443
1mbtFADUDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.443
1mvsDTMDihydrofolate reductase1.5.1.30.443
1x1cSAHC-20 methyltransferase/0.443
2bd0NAPSepiapterin reductase/0.443
2bjaNAD1-pyrroline-5-carboxylate dehydrogenase/0.443
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
2vd0D27Hematopoietic prostaglandin D synthase/0.443
2xc3RT8Steroid C26-monooxygenase1.14.13.1410.443
3c212BADNA integrity scanning protein DisA/0.443
4m10ICDProstaglandin G/H synthase 21.14.99.10.443
5cb5APRO-acetyl-ADP-ribose deacetylase/0.443
1dd6MCIMetallo-beta-lactamase type 2/0.442
1jpaANPEphrin type-B receptor 22.7.10.10.442
1uzwCDHIsopenicillin N synthase1.21.3.10.442
1w49APCNTPase P4/0.442
1xddAAYIntegrin alpha-L/0.442
3g4lROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
3k4nFADPyranose 2-oxidase/0.442
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.442
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.442
4xznNAPAldo-keto reductase family 1 member B101.1.10.442
1egdFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.441
1ot7IU5Bile acid receptor/0.441
1tllNAPNitric oxide synthase, brain1.14.13.390.441
1u1gBBBUridine phosphorylase2.4.2.30.441
1xagNAD3-dehydroquinate synthase/0.441
1xkdNAPIsocitrate dehydrogenase [NADP]/0.441
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
2yutNAPPutative short-chain oxidoreductase/0.441
3anmSYD1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.441
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3r8vZ62Cyclin-dependent kinase 22.7.11.220.441
3rupADPBiotin carboxylase6.3.4.140.441
4mq12C3Dual specificity tyrosine-phosphorylation-regulated kinase 1A2.7.12.10.441
4rvuNDPProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)/0.441
5kf9ACOPredicted acetyltransferase/0.441
1oaaNAPSepiapterin reductase1.1.1.1530.440
1v5eFADPyruvate oxidase/0.440
2eklNADD-3-phosphoglycerate dehydrogenase/0.440
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
2yj5ATPCopper-transporting ATPase/0.440
3ox4NADAlcohol dehydrogenase 21.1.1.10.440
3ru9NADUDP-N-acetylglucosamine 4-epimerase/0.440
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.440
3wg6NDPNADPH-dependent conjugated polyketone reductase C1/0.440
4bcoT6QCyclin-dependent kinase 22.7.11.220.440
4ev0CMPCyclic AMP receptor protein/0.440
4ful0VUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4h2nFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.440
4v37NADBetaine aldehyde dehydrogenase, chloroplastic1.2.1.80.440
4xivADPChemotaxis protein CheA2.7.13.30.440
5hwsNAP2-dehydropantoate 2-reductase/0.440
5kf2ACOPredicted acetyltransferase/0.440