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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
1n9nFMNPutative blue light receptor

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1n9nFMNPutative blue light receptor/1.000
1n9lFMNPutative blue light receptor/0.657
2z6dFMNPhototropin-22.7.11.10.629
4eetFMNPhototropin-22.7.11.10.616
4hiaFMNLOV protein/0.605
2pd7FADVivid PAS protein VVD/0.580
2pd8FADVivid PAS protein VVD/0.580
5djtFMNNPH1-2/0.578
3is2FADVivid PAS protein VVD/0.577
4hj6FMNLOV protein/0.571
2z6cFMNPhototropin-12.7.11.10.569
4r38RBFBlue-light-activated histidine kinase 22.7.13.30.569
3t50FMNBlue-light-activated histidine kinase2.7.13.30.563
2pr5FMNBlue-light photoreceptor/0.559
4eesFMNPhototropin-22.7.11.10.557
4hj4FMNLOV protein/0.550
3sw1FMNSensory box protein/0.549
5j3wFMNSensory box protein/0.547
2pdtFADVivid PAS protein VVD/0.543
4kukRBFPutative blue-light photoreceptor/0.543
4eeuFMNPhototropin-22.7.11.10.542
3d72FADVivid PAS protein VVD/0.540
3ue6FMNAureochrome1/0.536
3hjkFADVivid PAS protein VVD/0.535
3p7nFMNLight-activated DNA-binding protein EL222/0.535
4eepFMNPhototropin-22.7.11.10.534
5j4eFMNSensory box protein/0.534
4wujFMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy/0.532
4eerFMNPhototropin-22.7.11.10.530
5dkkFMNPredicted protein/0.528
4hhdFMNPhototropin-12.7.11.10.520
4kuoRBFPutative blue-light photoreceptor/0.513
4hnbFMNLOV protein/0.507
4hj3FMNLOV protein/0.501
1g28FMNPHY3/0.500
4yswFADXanthine dehydrogenase/oxidase/0.497
2v1aFMNNPH1-1/0.494
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.492
2briANPUridylate kinase2.7.4.220.489
1xddAAYIntegrin alpha-L/0.488
2ejvNADL-threonine 3-dehydrogenase/0.488
5efwFMNNPH1-1/0.488
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.485
3gmbFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.481
4z26FADPutative GMC-type oxidoreductase R13510.481
2q61SF1Peroxisome proliferator-activated receptor gamma/0.480
2xvv9DNSerum albumin/0.479
3s79ASDAromatase1.14.14.140.477
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.477
1kvsUPGUDP-glucose 4-epimerase5.1.3.20.476
2udpUPPUDP-glucose 4-epimerase5.1.3.20.474
4e4qRRHPeroxisome proliferator-activated receptor gamma/0.474
4qecNAPElxO/0.474
4ienCOAPutative acyl-CoA hydrolase/0.473
4du82P0Mevalonate diphosphate decarboxylase/0.471
2pvhP19Casein kinase II subunit alpha2.7.11.10.470
3juqAJDPhenazine biosynthesis protein A/B/0.470
4cukNAID-lactate dehydrogenase/0.470
1g1aNADdTDP-glucose 4,6-dehydratase/0.468
1rdwLARActin, alpha skeletal muscle/0.466
3cgfJNFMitogen-activated protein kinase 102.7.11.240.466
3nbvANPKetohexokinase/0.466
3qttANPPantothenate synthetase/0.466
3zlmANPAdenosine monophosphate-protein transferase NmFic2.7.7.n10.466
4wudANPDNA gyrase subunit B/0.466
2jlcTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.465
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.464
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.464
3t3r9PLCytochrome P450 2A61.14.130.464
4h4qFADBiphenyl dioxygenase ferredoxin reductase subunit/0.464
2p4yC03Peroxisome proliferator-activated receptor gamma/0.463
2v0uFMNNPH1-1/0.463
3zv64HBCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase1.3.1.560.463
4ejgNCTCytochrome P450 2A131.14.14.10.463
4zohFADPutative oxidoreductase FAD-binding subunit/0.463
1kvtUPGUDP-glucose 4-epimerase5.1.3.20.462
4jldADPAdenylate kinase/0.462
4jy2FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.462
4rpgFADUDP-galactopyranose mutase5.4.99.90.462
1m0wANPGlutathione synthetase6.3.2.30.461
3kb1ADPIron-sulfur cluster carrier protein/0.461
1osvCHCBile acid receptor/0.460
2ycfYCFSerine/threonine-protein kinase Chk22.7.11.10.460
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.460
4eji0QACytochrome P450 2A131.14.14.10.460
1efzPRFQueuine tRNA-ribosyltransferase2.4.2.290.459
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.459
1ipeNDPTropinone reductase 21.1.1.2360.459
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.459
3au8NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.459
4a4vYFDPeroxisome proliferator-activated receptor gamma/0.459
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.459
4bfsZVSPantothenate kinase2.7.1.330.459
4k28NADShikimate dehydrogenase family protein/0.459
1a9yUPGUDP-glucose 4-epimerase5.1.3.20.458
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.458
2hckQUETyrosine-protein kinase HCK2.7.10.20.458
3e8nVRADual specificity mitogen-activated protein kinase kinase 12.7.12.20.458
3epoMP5Phosphomethylpyrimidine synthase/0.458
3lu1NADUDP-N-acetylglucosamine 4-epimerase/0.458
3t3q9PLCytochrome P450 2A61.14.130.458
4dmmNAP3-oxoacyl-[acyl-carrier-protein] reductase/0.458
4fuyEK2Mitogen-activated protein kinase 12.7.11.240.458
1a80NDP2,5-diketo-D-gluconic acid reductase A1.1.1.3460.457
1gc5ADPADP-dependent glucokinase2.7.1.1470.457
1jpaANPEphrin type-B receptor 22.7.10.10.457
1q8yADPSerine/threonine-protein kinase SKY12.7.11.10.457
1xelUPGUDP-glucose 4-epimerase5.1.3.20.457
4nieNBHNuclear receptor ROR-gamma/0.457
4r3aRBFBlue-light-activated histidine kinase 22.7.13.30.457
2d1cNAPIsocitrate dehydrogenase [NADP]1.1.1.420.456
2lfoGCHFatty acid-binding protein, liver/0.456
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.456
2qenADPWalker-Type ATPase/0.456
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.456
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.456
4jazSTLPeroxisome proliferator-activated receptor gamma/0.456
4nmdFDABifunctional protein PutA/0.456
5dg3U21Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase/0.456
1ot7CHCBile acid receptor/0.455
2xhd7T9Glutamate receptor 2/0.455
2yy7NADL-threonine dehydrogenase/0.455
2z4sADPChromosomal replication initiator protein DnaA/0.455
4nxxGDPMitochondrial dynamics protein MID51/0.455
4oa9ANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.455
1i3mUD1UDP-glucose 4-epimerase/0.454
1pnvTYDdTDP-epi-vancosaminyltransferase2.4.1.3110.454
2freFMNNAD(P)H-flavin oxidoreductase/0.454
3b9lAZZSerum albumin/0.454
3coy53HPantothenate synthetase6.3.2.10.454
3fhxPXLPyridoxal kinase2.7.1.350.454
3fwjCAMCamphor 5-monooxygenase1.14.15.10.454
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.454
4hee14RPeroxisome proliferator-activated receptor gamma/0.454
4i8x6P3L-lactate dehydrogenase A chain1.1.1.270.454
5ej9TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.454
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.453
1udaUFGUDP-glucose 4-epimerase5.1.3.20.453
2bxmIMNSerum albumin/0.453
2qa1FADPgaE/0.453
3lpkZ76Beta-secretase 13.4.23.460.453
3of4FMNNitroreductase/0.453
3triNAPPyrroline-5-carboxylate reductase/0.453
4kzoNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.453
4wjiNAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase/0.453
1a5uATPPyruvate kinase PKM2.7.1.400.452
1glbADPGlycerol kinase/0.452
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.452
1necFMNOxygen-insensitive NAD(P)H nitroreductase10.452
1o76CAMCamphor 5-monooxygenase1.14.15.10.452
3jynNDPQuinone oxidoreductase/0.452
3ld6BCDLanosterol 14-alpha demethylase1.14.13.700.452
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.452
4bfvZVVPantothenate kinase2.7.1.330.452
4xumIMNPeroxisome proliferator-activated receptor gamma/0.452
1lf3EH5Plasmepsin-23.4.23.390.451
3l9hEMQKinesin-like protein KIF11/0.451
3pj8404Cyclin-dependent kinase 22.7.11.220.451
3pxvFMNNitroreductase/0.451
3wecAUICytochrome P450/0.451
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.451
4h3j10WBeta-secretase 13.4.23.460.451
2g8yNADHydroxycarboxylate dehydrogenase B/0.450
2w7xD1ASerine/threonine-protein kinase Chk22.7.11.10.450
3glmCOOGlutaconyl-CoA decarboxylase alpha subunit/0.450
3vsoEK1Peroxisome proliferator-activated receptor gamma/0.450
4fj0NAP17beta-hydroxysteroid dehydrogenase/0.450
5dp2NAPCurF/0.450
1dz6CAMCamphor 5-monooxygenase1.14.15.10.449
1e94ANPATP-dependent protease ATPase subunit HslU/0.449
1ofgNDPGlucose--fructose oxidoreductase1.1.99.280.449
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.449
2pym1UNGag-Pol polyprotein3.4.23.160.449
2ywwATPAspartate carbamoyltransferase regulatory chain/0.449
3h06VBPGlutamate receptor 2/0.449
3qaaG04Gag-Pol polyprotein3.4.23.160.449
3tdwGDPGentamicin resistance protein/0.449
3zoiM2WIsopenicillin N synthase1.21.3.10.449
1meiXMPInosine-5'-monophosphate dehydrogenase/0.448
1ppjANYCytochrome b/0.448
1u3cFADCryptochrome-1/0.448
1vfrFMNMajor NAD(P)H-flavin oxidoreductase1.6.990.448
2aa3AP0L-lactate dehydrogenase/0.448
2dv4SAHDiphthine synthase/0.448
3hwxTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.448
3iodA6DPantothenate synthetase6.3.2.10.448
3mdmFJZCholesterol 24-hydroxylase/0.448
3pjuC2EDiguanylate cyclase/phosphodiesterase/0.448
4ew2DXYTrifunctional purine biosynthetic protein adenosine-32.1.2.20.448
4l98LRGPeroxisome proliferator-activated receptor gamma/0.448
4nmcFADBifunctional protein PutA/0.448
5i4nATPTyrosine-protein kinase JAK2/0.448
1l8qADPChromosomal replication initiator protein DnaA/0.447
1vl8NAPOxidoreductase, short chain dehydrogenase/reductase family/0.447
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.447
2j09FMNDeoxyribodipyrimidine photo-lyase4.1.99.30.447
3d8vUD1Bifunctional protein GlmU/0.447
3gc9B45Mitogen-activated protein kinase 112.7.11.240.447
3rm618ZCyclin-dependent kinase 22.7.11.220.447
3uwqU5POrotidine 5'-phosphate decarboxylase/0.447
4em9TCEPeroxisome proliferator-activated receptor gamma/0.447
4prxADPDNA gyrase subunit B/0.447
4qe6JN3Bile acid receptor/0.447
4xf7ACPCarbohydrate/pyrimidine kinase, PfkB family/0.447
5ejaTD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.447
1nvtNAPShikimate dehydrogenase (NADP(+))/0.446
2fvlNAPAldo-keto reductase family 1 member C41.1.1.2250.446
2mwgFMNBlue-light photoreceptor/0.446
2rhrEMOPutative ketoacyl reductase1.3.10.446
2y9qANPMitogen-activated protein kinase 12.7.11.240.446
3bbrBHYGlutamate receptor 2/0.446
3rucNADUDP-N-acetylglucosamine 4-epimerase/0.446
3umvFADDeoxyribodipyrimidine photo-lyase4.1.99.30.446
4cbqNDPThioredoxin reductase/0.446
4oauADP2-5A-dependent ribonuclease3.1.260.446
4zseANPEpidermal growth factor receptor2.7.10.10.446
5ej4TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.446
1dg8NDPDihydrofolate reductase1.5.1.30.445
1j7kATPHolliday junction ATP-dependent DNA helicase RuvB/0.445
1me6IVSPlasmepsin-23.4.23.390.445
1t87CAMCamphor 5-monooxygenase1.14.15.10.445
1zc3GNPRas-related protein Ral-A/0.445
2bxqIMNSerum albumin/0.445
2x7bCOAN-alpha-acetyltransferase2.3.10.445
2ym2FADPhenylacetone monooxygenase1.14.13.920.445
2yylFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.445
3tk3CPZCytochrome P450 2B41.14.14.10.445
4fvqATPTyrosine-protein kinase JAK2/0.445
4jlcSU6Serine/threonine-protein kinase TBK12.7.11.10.445
5kjfNAJAlcohol dehydrogenase E chain1.1.1.10.445
1ae1NAPTropinone reductase 1/0.444
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.444
2eklNADD-3-phosphoglycerate dehydrogenase/0.444
4cp4CAMCamphor 5-monooxygenase1.14.15.10.444
4fj2NAP17beta-hydroxysteroid dehydrogenase/0.444
4gvjADPNon-receptor tyrosine-protein kinase TYK22.7.10.20.444
4hjfC2EGGDEF family protein/0.444
4ikeADPAdenylate kinase/0.444
4lxhC1EAlpha/beta hydrolase fold/0.444
4oagADPMitochondrial dynamics protein MID51/0.444
4ux9ANPMitogen-activated protein kinase 82.7.11.240.444
5bsgNAPPyrroline-5-carboxylate reductase/0.444
1qpjSTUTyrosine-protein kinase Lck2.7.10.20.443
1sxjADPReplication factor C subunit 5/0.443
2x7hPFNProstaglandin reductase 310.443
2y0mACOHistone acetyltransferase KAT8/0.443
3cppCAMCamphor 5-monooxygenase1.14.15.10.443
3rak03ZCyclin-dependent kinase 22.7.11.220.443
3t99ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.443
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.443
4fv6E57Mitogen-activated protein kinase 12.7.11.240.443
4lb2DM5Serum albumin/0.443
4m4922YL-lactate dehydrogenase A chain1.1.1.270.443
4n9iPCGCatabolite expression activator/0.443
4xj3GTPCyclic GMP-AMP synthase/0.443
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.442
1adcPADAlcohol dehydrogenase E chain1.1.1.10.442
1bdlIM1Gag-Pol polyprotein3.4.23.160.442
1bw9NADPhenylalanine dehydrogenase/0.442
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.442
1pxpCK8Cyclin-dependent kinase 22.7.11.220.442
2c27ACOMycothiol acetyltransferase2.3.1.1890.442
2vz6FEFCalcium/calmodulin-dependent protein kinase type II subunit alpha2.7.11.170.442
3cs8BRLPeroxisome proliferator-activated receptor gamma/0.442
3lqfNADGalactitol dehydrogenase/0.442
4bfzZVZPantothenate kinase2.7.1.330.442
4e5yNDPGDP-L-fucose synthase1.1.1.2710.442
4mq12C3Dual specificity tyrosine-phosphorylation-regulated kinase 1A2.7.12.10.442
4prvADPDNA gyrase subunit B/0.442
4riyADPEpidermal growth factor receptor2.7.10.10.442
5ej7TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.442
1i2bNADUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.441
1qorNDPQuinone oxidoreductase 1/0.441
1u28NAPNAD(P) transhydrogenase subunit beta1.6.1.20.441
1wvgAPRCDP-glucose 4,6-dehydratase4.2.1.450.441
2ep7NADGlyceraldehyde-3-phosphate dehydrogenase/0.441
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.441
2izrBRKCasein kinase I isoform gamma-32.7.11.10.441
2oegUPGUDP-glucose pyrophosphorylase/0.441
2zseACPPantothenate kinase2.7.1.330.441
3ge6FMNNitroreductase/0.441
3l63CAMCamphor 5-monooxygenase1.14.15.10.441
3tjsD0RCytochrome P450 3A4/0.441
3x22FMNOxygen-insensitive NAD(P)H nitroreductase/0.441
4c77N01Phenylacetone monooxygenase1.14.13.920.441
4g3rCAMCamphor 5-monooxygenase1.14.15.10.441
4l6gCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.441
5f54TMPSingle-stranded-DNA-specific exonuclease/0.441
1hihC20Gag-Pol polyprotein/0.440
1icuFMNOxygen-insensitive NAD(P)H nitroreductase/0.440
1juvNDPDihydrofolate reductase1.5.1.30.440
1orrNADCDP-paratose 2-epimerase/0.440
1rbmKT5Trifunctional purine biosynthetic protein adenosine-32.1.2.20.440
3af3GCPPantothenate kinase2.7.1.330.440
3iw1ASDSteroid C26-monooxygenase1.14.13.1410.440
3nl6TPSUncharacterized protein/0.440
3ortAGSSerine/threonine protein kinase/0.440
3pm0BHFCytochrome P450 1B1/0.440
3qwfNAP17beta-hydroxysteroid dehydrogenase/0.440
3rouCMPcAMP-activated global transcriptional regulator CRP/0.440
3wfjNAD2-dehydropantoate 2-reductase/0.440
4b8zNAPGDP-L-fucose synthase1.1.1.2710.440
4bfxZVXPantothenate kinase2.7.1.330.440
4jlk1NODeoxycytidine kinase2.7.1.740.440
4k33ACPFibroblast growth factor receptor 32.7.10.10.440
4o1pANPRibonuclease L/0.440
4up3NDPThioredoxin reductase/0.440