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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
1l4mNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.21

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1l4mNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.211.000
1l4kNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.758
1l4fNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.712
1l4hNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.694
1l4lNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.690
1jhaAAMNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.675
1d0vRBZNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.669
1jhoRMBNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.639
1l5oNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.613
1l4gNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.612
1jhrP2PNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.607
1l4eRBZNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.606
1l5k1RBNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.604
1l5l7RPNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.536
2qo9ANPEphrin type-A receptor 32.7.10.10.491
4g2fC07Ephrin type-A receptor 32.7.10.10.484
2q61SF1Peroxisome proliferator-activated receptor gamma/0.479
1pdhFASp-hydroxybenzoate hydroxylase/0.478
1jhqPMONicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.477
1l5m7RANicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.475
2givACOHistone acetyltransferase KAT8/0.473
3mdmFJZCholesterol 24-hydroxylase/0.472
4xldBRLPeroxisome proliferator-activated receptor gamma/0.472
2ejjSAHDiphthine synthase/0.469
2q9fC3SCholesterol 24-hydroxylase/0.469
4gk3L87Ephrin type-A receptor 32.7.10.10.469
1dbvNADGlyceraldehyde-3-phosphate dehydrogenase/0.468
1mg5NAIAlcohol dehydrogenase1.1.1.10.466
1dz4CAMCamphor 5-monooxygenase1.14.15.10.465
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.465
4z0hNADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic1.2.1.120.465
5c7oNADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific1.2.1.120.465
1cjkFOKAdenylate cyclase type 2/0.464
1cjkFOKAdenylate cyclase type 5/0.464
1u8fNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.464
3p62FMNPentaerythritol tetranitrate reductase/0.464
2eglSAHDiphthine synthase/0.463
2nu9COASuccinate--CoA ligase [ADP-forming] subunit alpha6.2.1.50.463
3mvqNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.463
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.463
4du82P0Mevalonate diphosphate decarboxylase/0.463
2huqSAHDiphthine synthase/0.462
2xyuQ9GEphrin type-A receptor 42.7.10.10.462
2q5p241Peroxisome proliferator-activated receptor gamma/0.461
3opdHIEHeat shock protein 83/0.461
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.461
2hutSAHDiphthine synthase/0.460
2qbmCAMCamphor 5-monooxygenase1.14.15.10.460
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.460
4aa4QC0Mitogen-activated protein kinase 14/0.460
4ejmNAPPutative zinc-binding dehydrogenase/0.460
4tuvCPZCytochrome P450 1191.140.460
1cs4FOKAdenylate cyclase type 2/0.459
1cs4FOKAdenylate cyclase type 5/0.459
1ol7ADPAurora kinase A2.7.11.10.459
4jhz1KVBeta-glucuronidase3.2.1.310.459
1culFOKAdenylate cyclase type 2/0.458
1culFOKAdenylate cyclase type 5/0.458
1g4tFTPThiamine-phosphate synthase/0.458
2phkATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform2.7.11.190.458
4l4eCAMCamphor 5-monooxygenase1.14.15.10.458
1pd9CO4Dihydrofolate reductase1.5.1.30.457
2owuSAHDiphthine synthase/0.457
2vci2GJHeat shock protein HSP 90-alpha/0.457
2z3uCRRCytochrome P450/0.457
3a4vNADNDP-sugar epimerase/0.457
3hx4ANPCalmodulin-domain protein kinase 1/0.457
1cjtFOKAdenylate cyclase type 2/0.456
1cjtFOKAdenylate cyclase type 5/0.456
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.456
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.456
1uyuCAMCamphor 5-monooxygenase1.14.15.10.456
3b20NADGlyceraldehyde-3-phosphate dehydrogenase/0.456
3cgeCOACoenzyme A disulfide reductase/0.456
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.456
2a94AP0L-lactate dehydrogenase1.1.1.270.455
2p5fSAHDiphthine synthase/0.455
2wmuZYUSerine/threonine-protein kinase Chk12.7.11.10.455
2ww4ADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.455
3a1nNADNDP-sugar epimerase/0.455
4egh0OYHeat shock protein HSP 90-alpha/0.455
4ib4ERM5-hydroxytryptamine receptor 2B/0.455
4lhtCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.455
2dv4SAHDiphthine synthase/0.454
2el0SAHDiphthine synthase/0.454
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.454
3zh8C58Protein kinase C iota type2.7.11.130.454
4nmdFDABifunctional protein PutA/0.454
2a1oCAMCamphor 5-monooxygenase1.14.15.10.453
2jcxNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.453
2p2xSAHDiphthine synthase/0.453
2ylxFADPhenylacetone monooxygenase1.14.13.920.453
3otwCOAPhosphopantetheine adenylyltransferase/0.453
4fakSAMRibosomal RNA large subunit methyltransferase H/0.453
4q71FADBifunctional protein PutA/0.453
5ez7FADProbable FAD-dependent oxidoreductase PA4991/0.453
1phhFADp-hydroxybenzoate hydroxylase/0.452
1szjNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.452
1ykdCMPAdenylate cyclase/0.452
2cgpCMPcAMP-activated global transcriptional regulator CRP/0.452
2dv7SAHDiphthine synthase/0.452
2q631UNGag-Pol polyprotein3.4.23.160.452
2tpsTPSThiamine-phosphate synthase/0.452
3zuyTCHTransporter/0.452
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.452
4kip1R9Mitogen-activated protein kinase 14/0.452
4q72FADBifunctional protein PutA/0.452
4q73FADBifunctional protein PutA/0.452
1cbfSAHCobalt-precorrin-4 C(11)-methyltransferase2.1.1.2710.451
1fm6BRLPeroxisome proliferator-activated receptor gamma/0.451
1meiXMPInosine-5'-monophosphate dehydrogenase/0.451
1sxjADPReplication factor C subunit 5/0.451
1t2dNADL-lactate dehydrogenase1.1.1.270.451
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.451
2dv5SAHDiphthine synthase/0.451
2ek2SAHDiphthine synthase/0.451
2pcgSAHDiphthine synthase/0.451
2znpK55Peroxisome proliferator-activated receptor delta/0.451
2zuiCAMCamphor 5-monooxygenase1.14.15.10.451
3lqfNADGalactitol dehydrogenase/0.451
4hgs15GCasein kinase I isoform gamma-32.7.11.10.451
4nd4NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.451
4neuQ1AReceptor-interacting serine/threonine-protein kinase 12.7.11.10.451
4rcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.451
1g69TZPThiamine-phosphate synthase/0.450
1yrdCAMCamphor 5-monooxygenase1.14.15.10.450
2cgw3C3Serine/threonine-protein kinase Chk12.7.11.10.450
2emrSAHDiphthine synthase/0.450
2znq401Peroxisome proliferator-activated receptor delta/0.450
4e37NDPCatalase1.11.1.60.450
4lsmNADGlyceraldehyde-3-phosphate dehydrogenase/0.450
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.450
5koiNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.450
1dhiMTXDihydrofolate reductase1.5.1.30.449
1eyqNARChalcone--flavonone isomerase 15.5.1.60.449
1i7gAZ2Peroxisome proliferator-activated receptor alpha/0.449
1sowNADL-lactate dehydrogenase1.1.1.270.449
2e07SAHDiphthine synthase/0.449
2feuCAMCamphor 5-monooxygenase1.14.15.10.449
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.449
2p5cSAHDiphthine synthase/0.449
2pcmSAHDiphthine synthase/0.449
2x0rNADMalate dehydrogenase/0.449
2ym3YM3Serine/threonine-protein kinase Chk12.7.11.10.449
3v1yNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.449
4aacAAVMitogen-activated protein kinase 14/0.449
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.449
4hj6FMNLOV protein/0.449
4y8wSTRSteroid 21-hydroxylase/0.449
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.448
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.448
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.448
1m76CAAHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.448
1o76CAMCamphor 5-monooxygenase1.14.15.10.448
1v35NAIEnoyl-ACP reductase/0.448
1zemNADXylitol dehydrogenase/0.448
2bdf24AProto-oncogene tyrosine-protein kinase Src2.7.10.20.448
2dv3SAHDiphthine synthase/0.448
2ed5SAHDiphthine synthase/0.448
2vcj2EQHeat shock protein HSP 90-alpha/0.448
3h6vNS6Glutamate receptor 2/0.448
3nwq2NCGag-Pol polyprotein3.4.23.160.448
3qn8NI7Gag-Pol polyprotein3.4.23.160.448
3toxNAPPutative oxidoreductase/0.448
4z07PCGcGMP-dependent protein kinase 12.7.11.120.448
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
2cahNDPCatalase1.11.1.60.447
2cgx3D3Serine/threonine-protein kinase Chk12.7.11.10.447
2hr8SAHDiphthine synthase/0.447
2owkSAHDiphthine synthase/0.447
2pcaSAHDiphthine synthase/0.447
2vbdV10Isopenicillin N synthase1.21.3.10.447
3cgcFADCoenzyme A disulfide reductase/0.447
3cgdCOACoenzyme A disulfide reductase/0.447
3fp0FP015-O-acetyltransferase/0.447
3pwrROCGag-Pol polyprotein3.4.23.160.447
3t113T1Gag-Pol polyprotein3.4.23.160.447
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.447
4o63NADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.447
5eypLOCTubulin beta chain/0.447
1booSAHModification methylase PvuII2.1.1.1130.446
2el3SAHDiphthine synthase/0.446
2gqwFADFerredoxin reductase/0.446
2w3bNDPDihydrofolate reductase1.5.1.30.446
3f1kNAPUncharacterized oxidoreductase YciK10.446
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.446
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.446
4xumIMNPeroxisome proliferator-activated receptor gamma/0.446
1bwsNDPGDP-L-fucose synthase/0.445
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.445
1k6pXN3Gag-Pol polyprotein3.4.23.160.445
1k6tXN1Gag-Pol polyprotein3.4.23.160.445
1okzUCN3-phosphoinositide-dependent protein kinase 12.7.11.10.445
1t85CAMCamphor 5-monooxygenase1.14.15.10.445
2egsSAHDiphthine synthase/0.445
2eh4SAHDiphthine synthase/0.445
2ek3SAHDiphthine synthase/0.445
2g2zCOZMalonyl CoA-acyl carrier protein transacylase2.3.1.390.445
2ivvPP1Proto-oncogene tyrosine-protein kinase receptor Ret2.7.10.10.445
2x2mX2MProto-oncogene tyrosine-protein kinase receptor Ret2.7.10.10.445
3gobHXXDdmC/0.445
3iaeD7KBenzaldehyde lyase/0.445
3il1B5DGlutamate receptor 2/0.445
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.445
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.445
3oibFDAPutative acyl-CoA dehydrogenase/0.445
4c9pCAMCytochrome P450/0.445
4h3f10OBeta-secretase 13.4.23.460.445
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.445
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.445
1k74544Peroxisome proliferator-activated receptor gamma/0.444
1phePIYCamphor 5-monooxygenase1.14.15.10.444
1pzgA3DLactate dehydrogenase/0.444
1tehNADAlcohol dehydrogenase class-31.1.1.10.444
2emuSAHDiphthine synthase/0.444
2oapANPType II secretion system protein (GspE-2)/0.444
2ou2ACOHistone acetyltransferase KAT5/0.444
2owvSAHDiphthine synthase/0.444
2wmxZY6Serine/threonine-protein kinase Chk12.7.11.10.444
2ylzFADPhenylacetone monooxygenase1.14.13.920.444
3adaNADSubunit alpha of sarocosine oxidase/0.444
3cgbCOACoenzyme A disulfide reductase/0.444
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.444
3s79ASDAromatase1.14.14.140.444
3tkiS25Serine/threonine-protein kinase Chk12.7.11.10.444
3wrhCAMCamphor 5-monooxygenase1.14.15.10.444
4boyNADGlyceraldehyde-3-phosphate dehydrogenase/0.444
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.444
4g95OAGDihydrofolate reductase1.5.1.30.444
4ia7BIVVitamin D3 receptor A/0.444
1dz6CAMCamphor 5-monooxygenase1.14.15.10.443
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.443
1j0xNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.443
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
1owpFADDeoxyribodipyrimidine photo-lyase4.1.99.30.443
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
2a1nCAMCamphor 5-monooxygenase1.14.15.10.443
2acxANPG protein-coupled receptor kinase 62.7.11.160.443
2b53D23Cyclin-dependent kinase 22.7.11.220.443
2b7aIZATyrosine-protein kinase JAK2/0.443
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.443
2hmaSAMtRNA-specific 2-thiouridylase MnmA/0.443
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.443
2udpUPPUDP-glucose 4-epimerase5.1.3.20.443
2wotZZGTGF-beta receptor type-12.7.11.300.443
3fwgCAMCamphor 5-monooxygenase1.14.15.10.443
3nwxKVSGag-Pol polyprotein3.4.23.160.443
4an92P7Dual specificity mitogen-activated protein kinase kinase 12.7.12.20.443
4dbvNDPGlyceraldehyde-3-phosphate dehydrogenase/0.443
4fcq2N6Heat shock protein HSP 90-alpha/0.443
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.443
4i8vBHFCytochrome P450 1A11.14.14.10.443
4kl9NDPDihydrofolate reductase1.5.1.30.443
4wuoNAD3-isopropylmalate dehydrogenase1.1.1.850.443
2e08SAHDiphthine synthase/0.442
2e8hSAHDiphthine synthase/0.442
2egbSAHDiphthine synthase/0.442
2qblCAMCamphor 5-monooxygenase1.14.15.10.442
2rhgIGPTryptophan synthase alpha chain/0.442
2znnS44Peroxisome proliferator-activated receptor alpha/0.442
3b9lAZZSerum albumin/0.442
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.442
3wrmCAMCamphor 5-monooxygenase1.14.15.10.442
4cukNAID-lactate dehydrogenase/0.442
4enhFVXCholesterol 24-hydroxylase/0.442
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.442
4fswHK6Serine/threonine-protein kinase Chk12.7.11.10.442
4i8zG08Gag-Pol polyprotein3.4.23.160.442
4r8qADPMitotic checkpoint serine/threonine-protein kinase BUB12.7.11.10.442
1nvqUCNSerine/threonine-protein kinase Chk12.7.11.10.441
2ejkSAHDiphthine synthase/0.441
2en5SAHDiphthine synthase/0.441
2ep7NADGlyceraldehyde-3-phosphate dehydrogenase/0.441
2ghlLIBMitogen-activated protein kinase 14/0.441
2pchSAHDiphthine synthase/0.441
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.441
3bheBZNGag-Pol polyprotein3.4.23.160.441
3dmtNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.441
3qt62P0Mevalonate diphosphate decarboxylase/0.441
3u33FADPutative acyl-CoA dehydrogenase AidB1.3.990.441
3uyt0CKCasein kinase I isoform delta2.7.11.10.441
3w4yFADMitochondrial FAD-linked sulfhydryl oxidase ERV11.8.3.20.441
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.441
4ambDUDPutative glycosyl transferase/0.441
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.441
1bygSTUTyrosine-protein kinase CSK/0.440
1drhNAPDihydrofolate reductase1.5.1.30.440
1fm7DFVChalcone--flavonone isomerase 15.5.1.60.440
1h65GDPTranslocase of chloroplast 343.6.50.440
1hiiC20Gag-Pol polyprotein/0.440
1ie3NADMalate dehydrogenase/0.440
1k6cMK1Gag-Pol polyprotein3.4.23.160.440
1kl2FONSerine hydroxymethyltransferase/0.440
1olmVTQSEC14-like protein 2/0.440
1pl8NADSorbitol dehydrogenase1.1.1.140.440
1rekB8LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
1t88CAMCamphor 5-monooxygenase1.14.15.10.440
1y7lASN_LEU_ASN_ILECysteine synthase2.5.1.470.440
2e16SAHDiphthine synthase/0.440
2e7zMGDAcetylene hydratase/0.440
2huvSAHDiphthine synthase/0.440
2ibzUQ6Cytochrome b/0.440
2nruT12Interleukin-1 receptor-associated kinase 42.7.11.10.440
2q0lFADThioredoxin reductase1.8.1.90.440
2v9jATP5'-AMP-activated protein kinase subunit gamma-1/0.440
2ym5YM5Serine/threonine-protein kinase Chk12.7.11.10.440
2z6rSAHDiphthine synthase/0.440
2zawCAMCamphor 5-monooxygenase1.14.15.10.440
3ajrNADNDP-sugar epimerase/0.440
3fwiCAMCamphor 5-monooxygenase1.14.15.10.440
4ek1CAMCamphor 5-monooxygenase1.14.15.10.440
4ftcH6KSerine/threonine-protein kinase Chk12.7.11.10.440
4ftu7HKSerine/threonine-protein kinase Chk12.7.11.10.440
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.440
4iwq1FVSerine/threonine-protein kinase TBK12.7.11.10.440
4l4fCAMCamphor 5-monooxygenase1.14.15.10.440