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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
2dw0GM6Zinc metalloproteinase-disintegrin-like VAP2B3.4.24

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2dw0GM6Zinc metalloproteinase-disintegrin-like VAP2B3.4.241.000
1mncPLHNeutrophil collagenase3.4.24.340.535
2oxwILE_ALA_GLYMacrophage metalloelastase3.4.24.650.535
4gr8R4CMacrophage metalloelastase3.4.24.650.535
1dthBATSnake venom metalloproteinase atrolysin-D3.4.24.420.527
1zvxFINNeutrophil collagenase3.4.24.340.522
3kek3EKCollagenase 33.4.240.519
2wo8077Macrophage metalloelastase3.4.24.650.517
2w13WR2Snake venom metalloproteinase BaP13.4.240.515
1bzsBSINeutrophil collagenase3.4.24.340.514
2w14WR2Snake venom metalloproteinase BaP13.4.240.513
3aig0ZCSnake venom metalloproteinase adamalysin-23.4.24.460.509
3tskQEGMacrophage metalloelastase3.4.24.650.503
4g9lNGHStromelysin-13.4.24.170.503
1atl0QISnake venom metalloproteinase atrolysin-D3.4.24.420.502
2wo9068Macrophage metalloelastase3.4.24.650.502
3b8z294A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.502
3ljgEEFMacrophage metalloelastase3.4.24.650.502
2woa576Macrophage metalloelastase3.4.24.650.501
3i7g732Collagenase 33.4.240.496
1d7xSPCStromelysin-13.4.24.170.495
4guyKLJMacrophage metalloelastase3.4.24.650.495
3fwjCAMCamphor 5-monooxygenase1.14.15.10.492
1uttCP8Macrophage metalloelastase3.4.24.650.489
3fwgCAMCamphor 5-monooxygenase1.14.15.10.489
3hyg099A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.489
1qrrUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.488
3hy7097A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.488
1uyuCAMCamphor 5-monooxygenase1.14.15.10.487
3likEEGMacrophage metalloelastase3.4.24.650.487
4an4DUDPutative glycosyl transferase/0.487
4l4eCAMCamphor 5-monooxygenase1.14.15.10.487
2jih097A disintegrin and metalloproteinase with thrombospondin motifs 13.4.240.485
2ovx4MRMatrix metalloproteinase-93.4.24.350.485
1g05BBHStromelysin-13.4.24.170.484
3k4yIPEIsopentenyl phosphate kinase2.7.4.260.484
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.482
1hdoNAPFlavin reductase (NADPH)/0.479
2ow06MRMatrix metalloproteinase-93.4.24.350.479
3ohoZ79Stromelysin-13.4.24.170.479
1biwS80Stromelysin-13.4.24.170.478
1iy8NADLevodione reductase/0.478
2ovz5MRMatrix metalloproteinase-93.4.24.350.477
3ddw055Glycogen phosphorylase, liver form2.4.1.10.477
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.477
1jk3BATMacrophage metalloelastase3.4.24.650.476
3fwfCAMCamphor 5-monooxygenase1.14.15.10.476
3lxiCAMCytochrome P450/0.476
4gr0R4BMacrophage metalloelastase3.4.24.650.476
1rm8BATMatrix metalloproteinase-163.4.240.475
2d1nFA4Collagenase 33.4.240.475
3lgp50XDisintegrin and metalloproteinase domain-containing protein 173.4.24.860.475
4g3rCAMCamphor 5-monooxygenase1.14.15.10.475
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.474
2j7pGNPSignal recognition particle protein/0.474
2j7pGNPSignal recognition particle receptor FtsY/0.474
3l63CAMCamphor 5-monooxygenase1.14.15.10.474
3wrmCAMCamphor 5-monooxygenase1.14.15.10.474
4cp4CAMCamphor 5-monooxygenase1.14.15.10.473
1gkcNFHMatrix metalloproteinase-93.4.24.350.472
3e5hGNPRas-related protein Rab-28/0.472
2oy2ILE_ALA_GLYNeutrophil collagenase3.4.24.340.471
2rlcCHDCholoylglycine hydrolase3.5.1.240.471
4lhvGDPRas-related protein Rab-8A/0.471
2wo8023Macrophage metalloelastase3.4.24.650.470
1hv5RXPStromelysin-33.4.240.469
1m75CAAHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.469
3kkzSAMUncharacterized protein/0.469
4l4bCAMCamphor 5-monooxygenase1.14.15.10.469
4q0kGA3Phytohormone-binding protein/0.469
1dz8CAMCamphor 5-monooxygenase1.14.15.10.468
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.468
2i47KGYDisintegrin and metalloproteinase domain-containing protein 173.4.24.860.468
5ej6TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.468
3s79ASDAromatase1.14.14.140.467
4gr3R45Macrophage metalloelastase3.4.24.650.467
1t91GTPRas-related protein Rab-7a/0.466
1vi2NADQuinate/shikimate dehydrogenase/0.466
4lhtCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.466
1dz4CAMCamphor 5-monooxygenase1.14.15.10.465
3wrjCAMCamphor 5-monooxygenase1.14.15.10.465
4emtC2EStimulator of interferon genes protein/0.465
1dhfFOLDihydrofolate reductase1.5.1.30.464
1mg5NAIAlcohol dehydrogenase1.1.1.10.464
2a1nCAMCamphor 5-monooxygenase1.14.15.10.464
3fhxPLPPyridoxal kinase2.7.1.350.464
3i6iNDPPutative leucoanthocyanidin reductase 1/0.464
1yrcCAMCamphor 5-monooxygenase1.14.15.10.463
2hk9NAPShikimate dehydrogenase (NADP(+))/0.463
4jc51K5Stimulator of interferon genes protein/0.463
1phhFADp-hydroxybenzoate hydroxylase/0.462
2i47INNDisintegrin and metalloproteinase domain-containing protein 173.4.24.860.462
4opgFDAConserved Archaeal protein/0.462
1bw9NADPhenylalanine dehydrogenase/0.461
1kvkATPMevalonate kinase2.7.1.360.461
2feuCAMCamphor 5-monooxygenase1.14.15.10.461
2y60M8FIsopenicillin N synthase1.21.3.10.461
2zaxCAMCamphor 5-monooxygenase1.14.15.10.461
4hxyNDPPlm1/0.461
4tm4FDAKtzI/0.461
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.460
2npaMMBPeroxisome proliferator-activated receptor alpha/0.460
3zxhE41Collagenase 33.4.240.460
4dpeNGHStromelysin-13.4.24.170.460
1t88CAMCamphor 5-monooxygenase1.14.15.10.459
2a1mCAMCamphor 5-monooxygenase1.14.15.10.459
2iviACWIsopenicillin N synthase1.21.3.10.459
3wrhCAMCamphor 5-monooxygenase1.14.15.10.459
4ejmNAPPutative zinc-binding dehydrogenase/0.459
1g1aNADdTDP-glucose 4,6-dehydratase/0.458
1hb3SCVIsopenicillin N synthase1.21.3.10.458
3drcMTXDihydrofolate reductase1.5.1.30.458
3l0tINNDisintegrin and metalloproteinase domain-containing protein 173.4.24.860.458
3zoiM2WIsopenicillin N synthase1.21.3.10.458
4bfvZVVPantothenate kinase2.7.1.330.458
4l4aCAMCamphor 5-monooxygenase1.14.15.10.458
4l6gCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.458
1me6IVSPlasmepsin-23.4.23.390.457
1xe65FPPlasmepsin-23.4.23.390.457
2dhfDZFDihydrofolate reductase1.5.1.30.457
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.457
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.457
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.457
1slnINHStromelysin-13.4.24.170.456
2ble5GPGMP reductase 1/0.456
3vsxR32Renin3.4.23.150.456
4fn4NADShort chain dehydrogenase/0.456
4lol1YEStimulator of interferon genes protein/0.456
1hb1OCVIsopenicillin N synthase1.21.3.10.455
1i59ADPChemotaxis protein CheA2.7.13.30.455
2fznFADBifunctional protein PutA1.5.5.20.455
2g1o2IGRenin3.4.23.150.455
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.455
1cg4IMOAdenylosuccinate synthetase/0.454
4b68FADL-ornithine N(5)-monooxygenase/0.454
4bb3KKAIsopenicillin N synthase1.21.3.10.454
5cp4CAMCamphor 5-monooxygenase1.14.15.10.454
1gebCAMCamphor 5-monooxygenase1.14.15.10.453
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.453
2w0dCGSMacrophage metalloelastase3.4.24.650.453
3ljtLA3A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.453
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.453
4eph0RKCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.453
4l4fCAMCamphor 5-monooxygenase1.14.15.10.453
1pwuGM6Lethal factor3.4.24.830.452
1w0kADPATP synthase subunit alpha, mitochondrial/0.452
1w0kADPATP synthase subunit beta, mitochondrial3.6.3.140.452
2c29NAPDihydroflavonol 4-reductase/0.452
2cppCAMCamphor 5-monooxygenase1.14.15.10.452
2g1r3IGRenin3.4.23.150.452
3zkyWT4Isopenicillin N synthase1.21.3.10.452
4zj8SUVOrexin receptor type 1/0.452
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.451
1i59ANPChemotaxis protein CheA2.7.13.30.451
1iwiCAMCamphor 5-monooxygenase1.14.15.10.451
1juvNDPDihydrofolate reductase1.5.1.30.451
1nzdUPGDNA beta-glucosyltransferase/0.451
2zz0FADThioredoxin reductase 1, cytoplasmic1.8.1.90.451
3c1oNAPEugenol synthase/0.451
4rvnCOAPhenylacetate-coenzyme A ligase/0.451
1nooCAHCamphor 5-monooxygenase1.14.15.10.450
2srtINHStromelysin-13.4.24.170.450
3gbk2PQPeroxisome proliferator-activated receptor gamma/0.450
4omaLCSMethionine gamma-lyase/0.450
4oztP1AEcdysone receptor, putative/0.450
5dw50T1Succinyl-CoA:acetate CoA-transferase/0.450
1zxcIH6Disintegrin and metalloproteinase domain-containing protein 173.4.24.860.449
2c27ACOMycothiol acetyltransferase2.3.1.1890.449
2v16C47Renin3.4.23.150.449
3cppCAMCamphor 5-monooxygenase1.14.15.10.449
3mjeNDPAmphB/0.449
3n0hTOPDihydrofolate reductase1.5.1.30.449
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.449
2a1oCAMCamphor 5-monooxygenase1.14.15.10.448
2bu9HFVIsopenicillin N synthase1.21.3.10.448
2bwpPLG5-aminolevulinate synthase2.3.1.370.448
2gs7ANPEpidermal growth factor receptor2.7.10.10.448
2jb4A14Isopenicillin N synthase1.21.3.10.448
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
2zawCAMCamphor 5-monooxygenase1.14.15.10.448
3och2MXDihydrofolate reductase1.5.1.30.448
4dpwAGSMevalonate diphosphate decarboxylase/0.448
4ef8FMNDihydroorotate dehydrogenase (fumarate)/0.448
4k28NADShikimate dehydrogenase family protein/0.448
4klaCHDFerrochelatase, mitochondrial4.99.1.10.448
4l49CAMCamphor 5-monooxygenase1.14.15.10.448
1d8mBBHStromelysin-13.4.24.170.447
2vbdV10Isopenicillin N synthase1.21.3.10.447
3ixp834Ecdysone receptor/0.447
3qizQI2Botulinum neurotoxin type A3.4.24.690.447
4i03L88Macrophage metalloelastase3.4.24.650.447
1bk0ACVIsopenicillin N synthase1.21.3.10.446
1dz6CAMCamphor 5-monooxygenase1.14.15.10.446
1h73ANPHomoserine kinase2.7.1.390.446
1i5cADPChemotaxis protein CheA2.7.13.30.446
1jkx138Phosphoribosylglycinamide formyltransferase/0.446
2jlcTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.446
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.446
3fwiCAMCamphor 5-monooxygenase1.14.15.10.446
3mzhCMPCRP-like cAMP-activated global transcriptional regulator/0.446
4dpy2P0Mevalonate diphosphate decarboxylase/0.446
5jlaNADPutative short-chain dehydrogenase/reductase/0.446
1pvgANPDNA topoisomerase 25.99.1.30.445
1uzwCDHIsopenicillin N synthase1.21.3.10.445
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.445
1youPFDCollagenase 33.4.240.445
2a94AP0L-lactate dehydrogenase1.1.1.270.445
2gjnFMNNitronate monooxygenase1.13.12.160.445
2rewREWPeroxisome proliferator-activated receptor alpha/0.445
2xs3ALA_PHE_THR_SERKarilysin3.4.240.445
3v9v21LPeroxisome proliferator-activated receptor gamma/0.445
4gah0ETAcyl-coenzyme A thioesterase THEM43.1.2.20.445
4imfSI3N-acetylneuraminate lyase/0.445
5idwNAPShort-chain dehydrogenase/reductase SDR/0.445
1b14NADAlcohol dehydrogenase1.1.1.10.444
1iwjCAMCamphor 5-monooxygenase1.14.15.10.444
1pq944BOxysterols receptor LXR-beta/0.444
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.444
2d1oFA4Stromelysin-13.4.24.170.444
3aw9NADNAD-dependent epimerase/dehydratase/0.444
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.444
3m6pBB2Peptide deformylase 1B, chloroplastic/mitochondrial3.5.1.880.444
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.444
3wagTYDGlycosyltransferase/0.444
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
4c9pCAMCytochrome P450/0.444
4dbzNDPPutative ketoacyl reductase1.3.10.444
4f9mFCMPeroxisome proliferator-activated receptor gamma/0.444
4fc7NAPPeroxisomal 2,4-dienoyl-CoA reductase1.3.1.340.444
4hlk431Tankyrase-22.4.2.300.444
4l0oPLPCystathionine gamma-synthase2.5.1.480.444
5koiNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
1cydNDPCarbonyl reductase [NADPH] 21.1.1.1840.443
1gd1NADGlyceraldehyde-3-phosphate dehydrogenase/0.443
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.443
2e0nSAHPrecorrin-2 C20-methyltransferase/0.443
2hu2NADC-terminal binding protein 1/0.443
2iko7IGRenin3.4.23.150.443
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.443
3gbuATPUncharacterized sugar kinase PH14592.7.10.443
3q8hAO92-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.443
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
3v9y24LPeroxisome proliferator-activated receptor gamma/0.443
4a8v2ANMajor pollen allergen Bet v 1-J/0.443
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4biwANPSensor histidine kinase CpxA/0.443
4egbNADdTDP-glucose 4,6-dehydratase/0.443
4qi5FADCellobiose dehydrogenase/0.443
6cp4CAMCamphor 5-monooxygenase1.14.15.10.443
1gqtACPRibokinase/0.442
2f3rG5PGuanylate kinase2.7.4.80.442
2vcmM11Isopenicillin N synthase1.21.3.10.442
2vesGVRUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.442
2w3bNDPDihydrofolate reductase1.5.1.30.442
2z97CAMCamphor 5-monooxygenase1.14.15.10.442
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.442
3pcrGTPADP-ribosylation factor 6/0.442
4a6nFADTetX family tetracycline inactivation enzyme/0.442
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.442
4j0v1H7Beta-secretase 13.4.23.460.442
4kgkGTPUncharacterized protein/0.442
4lxk1YTBeta-secretase 13.4.23.460.442
4wqmFADToluene-4-monooxygenase electron transfer component1.18.1.30.442
1b8yIN7Stromelysin-13.4.24.170.441
1dyiFOLDihydrofolate reductase1.5.1.30.441
1hfqMOTDihydrofolate reductase1.5.1.30.441
1pjkANPCasein kinase II subunit alpha2.7.11.10.441
1xddAAYIntegrin alpha-L/0.441
2ahcVNLChorismate pyruvate-lyase/0.441
2i7pACOPantothenate kinase 32.7.1.330.441
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.441
2y0mACOHistone acetyltransferase KAT8/0.441
4xyeNADFormate dehydrogenase/0.441
5eg3ACPFibroblast growth factor receptor 2/0.441
1bxdANPOsmolarity sensor protein EnvZ2.7.13.30.440
1mjaCOAHistone acetyltransferase ESA1/0.440
1t2bCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.440
1t86CAMCamphor 5-monooxygenase1.14.15.10.440
1w19T5P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
2aq7TL53-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.440
2b53D23Cyclin-dependent kinase 22.7.11.220.440
2e4nSAHDiphthine synthase/0.440
2hckQUETyrosine-protein kinase HCK2.7.10.20.440
2ozuACOHistone acetyltransferase KAT6A/0.440
2zuiCAMCamphor 5-monooxygenase1.14.15.10.440
3a4vNADNDP-sugar epimerase/0.440
3clyACPFibroblast growth factor receptor 2/0.440
3cukFADD-amino-acid oxidase1.4.3.30.440
3jpuTY4Transcriptional activator protein LasR/0.440
3kjm245Cytokinin dehydrogenase 11.5.99.120.440
3t3r9PLCytochrome P450 2A61.14.130.440
4br0AU1Ectonucleoside triphosphate diphosphohydrolase 2/0.440
4m9aFDAAcyl-CoA dehydrogenase/0.440
4nr42LKCREB-binding protein/0.440
4nvk2NYPeroxidase/0.440