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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
4cezO3NIntegrase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3zsrO3NIntegrase/1.000
4cezO3NIntegrase/1.000
4ceoG0TIntegrase/0.682
4ced9NSIntegrase/0.673
4cggK5QIntegrase/0.660
3zt0ZT0Integrase/0.652
4ceaZSWIntegrase/0.648
4cf8V7HIntegrase/0.641
4ceqQCHIntegrase/0.635
3zsvZSVIntegrase/0.630
4cebZSVIntegrase/0.630
4cfbOM3Integrase/0.626
3zswZSWIntegrase/0.625
4cjrFYMIntegrase/0.625
4cigX0PIntegrase/0.622
4ce9O3NIntegrase/0.617
4cerVL4Integrase/0.615
4cifJDXIntegrase/0.602
4cfaWOPIntegrase/0.600
3zsqO4NIntegrase/0.598
4cfc7NVIntegrase/0.598
4cgjNZLIntegrase/0.597
4cj3E4FIntegrase/0.597
4cgd8P3Integrase/0.593
4ck1OM1Integrase/0.593
4ck2NVUIntegrase/0.592
4cefD0TIntegrase/0.590
3zsyOM3Integrase/0.589
4cjfRVNIntegrase/0.588
4cghLOZIntegrase/0.587
4cjeQ31Integrase/0.584
4chyC5QIntegrase/0.582
4cjuJNSIntegrase/0.581
4cjsL0YIntegrase/0.580
4cgiNZLIntegrase/0.578
4cf0O5UIntegrase/0.576
3zszOM2Integrase/0.575
4cf23GMIntegrase/0.575
4cjp4D2Integrase/0.572
4cjqVXOIntegrase/0.570
4ceeB0TIntegrase/0.566
3zcmPX3Integrase/0.564
4cec2SSIntegrase/0.563
4cfdS8YIntegrase/0.563
4cjkH39Integrase/0.563
4cf1IY7Integrase/0.554
3zt2ZT2Integrase/0.547
4cieY7NIntegrase/0.546
3zt3ZT4Integrase/0.545
4ck3K1TIntegrase/0.544
4cesNFWIntegrase/0.543
4cj54VWIntegrase/0.542
3zsxN44Integrase/0.533
4chqCWUIntegrase/0.525
4cj4S3GIntegrase/0.523
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.497
3zt1OM1Integrase/0.495
1rx8FOLDihydrofolate reductase1.5.1.30.490
4mv8ACPBiotin carboxylase6.3.4.140.489
1m78NDPDihydrofolate reductase1.5.1.30.488
1rx8NAPDihydrofolate reductase1.5.1.30.484
3lqfNADGalactitol dehydrogenase/0.484
3mdvCL6Cholesterol 24-hydroxylase/0.481
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.481
3idsNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.477
3bhtMFRCyclin-dependent kinase 22.7.11.220.476
1ia3TQ5Dihydrofolate reductase1.5.1.30.475
3lsiFADPyranose 2-oxidase/0.475
4ure1PSCyclohexanol dehydrogenase/0.475
1nqoNADGlyceraldehyde-3-phosphate dehydrogenase/0.474
2rh9IGPTryptophan synthase alpha chain/0.472
4ejmNAPPutative zinc-binding dehydrogenase/0.471
1nzdUPGDNA beta-glucosyltransferase/0.469
4nbwNADShort-chain dehydrogenase/reductase SDR/0.469
1nq5NADGlyceraldehyde-3-phosphate dehydrogenase/0.468
2p5uNADUDP-glucose 4-epimerase/0.468
3d84NDPDihydrofolate reductase1.5.1.30.468
3fr8NDPKetol-acid reductoisomerase, chloroplastic1.1.1.860.467
1bwsNDPGDP-L-fucose synthase/0.466
1mvsDTMDihydrofolate reductase1.5.1.30.466
3tw6ADPPyruvate carboxylase/0.466
1ia1NDPDihydrofolate reductase1.5.1.30.465
2wxvWXVCyclin-dependent kinase 22.7.11.220.465
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.465
2c29NAPDihydroflavonol 4-reductase/0.464
2hamC33Vitamin D3 receptor/0.464
3cpsNADGlyceraldehyde-3-phosphate dehydrogenase/0.464
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.463
2vz6FEFCalcium/calmodulin-dependent protein kinase type II subunit alpha2.7.11.170.463
3ig6438Urokinase-type plasminogen activator3.4.21.730.463
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.463
1k8y13PTryptophan synthase alpha chain/0.462
3vtbTKAVitamin D3 receptor/0.462
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.462
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.462
1nzfUPGDNA beta-glucosyltransferase/0.461
3mtfA3FActivin receptor type-12.7.11.300.461
3own3OWRenin3.4.23.150.461
3qlrNDPDihydrofolate reductase1.5.1.30.461
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
1kfbIGPTryptophan synthase alpha chain/0.460
1xe65FPPlasmepsin-23.4.23.390.460
2nruT12Interleukin-1 receptor-associated kinase 42.7.11.10.460
4zlaBESCytosol aminopeptidase3.4.11.10.460
1s19MC9Vitamin D3 receptor/0.459
1s3uTQDDihydrofolate reductase1.5.1.30.459
3dogNNNCyclin-dependent kinase 22.7.11.220.459
1diuBDMDihydrofolate reductase1.5.1.30.458
3vfa031Gag-Pol polyprotein3.4.23.160.458
4c34STUcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.458
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.457
2bxmIMNSerum albumin/0.457
3och2MXDihydrofolate reductase1.5.1.30.457
5ajqDB8Serine/threonine-protein kinase 102.7.11.10.457
2gnhH52cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.456
2ohvNHLGlutamate racemase/0.456
3orfNADDihydropteridine reductase1.5.1.340.456
3p62FMNPentaerythritol tetranitrate reductase/0.456
3qlsNDPDihydrofolate reductase1.5.1.30.456
4g2fC07Ephrin type-A receptor 32.7.10.10.456
4q71FADBifunctional protein PutA/0.456
4qmzB49Serine/threonine-protein kinase 242.7.11.10.456
1bv9XV6Gag-Pol polyprotein3.4.23.160.455
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.455
2xyuQ9GEphrin type-A receptor 42.7.10.10.455
4fv6E57Mitogen-activated protein kinase 12.7.11.240.455
4ht2V50Carbonic anhydrase 124.2.1.10.455
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
1u4dDBQActivated CDC42 kinase 1/0.454
2w9hTOPDihydrofolate reductase1.5.1.30.454
5fwnNAPPutative dehydrogenase/0.454
1drhNAPDihydrofolate reductase1.5.1.30.453
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.453
2z0ySAMRibosomal RNA small subunit methyltransferase E/0.453
3hdmMMGSerine/threonine-protein kinase Sgk12.7.11.10.453
4ez30S0Cyclin-dependent kinase 22.7.11.220.453
4p8rNADGlyceraldehyde-3-phosphate dehydrogenase/0.453
4q72FADBifunctional protein PutA/0.453
4y93746Tyrosine-protein kinase/0.453
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.452
1jpaANPEphrin type-B receptor 22.7.10.10.452
1rkhVD2Vitamin D3 receptor/0.452
2d8aNADL-threonine 3-dehydrogenase/0.452
3ijdC2FMethylenetetrahydrofolate reductase/0.452
3qt62P0Mevalonate diphosphate decarboxylase/0.452
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.451
2dhfDZFDihydrofolate reductase1.5.1.30.451
2q70DC8Estrogen receptor/0.451
3iaeD7KBenzaldehyde lyase/0.451
3s7a684Dihydrofolate reductase1.5.1.30.451
4an4DUDPutative glycosyl transferase/0.451
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
4dptAGSMevalonate diphosphate decarboxylase/0.451
4o59NADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.451
1lp4ANPCasein kinase II subunit alpha2.7.11.10.450
1py5PY1TGF-beta receptor type-12.7.11.300.450
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
1qvnFRIInterleukin-2/0.450
3a7jADPSerine/threonine-protein kinase 242.7.11.10.450
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
3gggNADPrephenate dehydrogenase/0.450
3t3c017Gag-Pol polyprotein3.4.23.160.450
4aqc88ATyrosine-protein kinase JAK2/0.450
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.450
4h1m0YJProtein-tyrosine kinase 2-beta2.7.10.20.450
4i6gFADCryptochrome-2/0.450
1m2qMNXCasein kinase II subunit alpha2.7.11.10.449
1zemNADXylitol dehydrogenase/0.449
2rhgIGPTryptophan synthase alpha chain/0.449
2xs0ANPMitogen-activated protein kinase 82.7.11.240.449
3a783EVVitamin D3 receptor/0.449
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.449
3zuyTCHTransporter/0.449
4fg8ATPCalcium/calmodulin-dependent protein kinase type 12.7.11.170.449
4k28NADShikimate dehydrogenase family protein/0.449
4u9aSTUInterleukin-1 receptor-associated kinase 42.7.11.10.449
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.449
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.448
1metDMPGag-Pol polyprotein3.4.23.160.448
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.448
2feuCAMCamphor 5-monooxygenase1.14.15.10.448
2gjlFMNNitronate monooxygenase1.13.12.160.448
2izrBRKCasein kinase I isoform gamma-32.7.11.10.448
2q9fC3SCholesterol 24-hydroxylase/0.448
2ylzFADPhenylacetone monooxygenase1.14.13.920.448
3koo24DBifunctional epoxide hydrolase 23.3.2.100.448
4m87NADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.448
5ax35IDMitogen-activated protein kinase 12.7.11.240.448
1bdrIM1Gag-Pol polyprotein3.4.23.160.447
1h51FMNPentaerythritol tetranitrate reductase/0.447
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.447
2qo9ANPEphrin type-A receptor 32.7.10.10.447
2tpsTPSThiamine-phosphate synthase/0.447
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.447
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.447
3rk507ZCyclin-dependent kinase 22.7.11.220.447
3vwdACOAlpha-tubulin N-acetyltransferase 1/0.447
3w5hFADNADH-cytochrome b5 reductase 31.6.2.20.447
4b8wNAPGDP-L-fucose synthase1.1.1.2710.447
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.447
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1poxFADPyruvate oxidase1.2.3.30.446
1rfvADPPyridoxal kinase2.7.1.350.446
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.446
2dfvNADL-threonine 3-dehydrogenase/0.446
2drcMTXDihydrofolate reductase1.5.1.30.446
2qbmCAMCamphor 5-monooxygenase1.14.15.10.446
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.446
3p8zSAHGenome polyprotein2.1.1.560.446
4enhFVXCholesterol 24-hydroxylase/0.446
4jin1L7RIO-type serine/threonine-protein kinase Rio12.7.11.10.446
4q73FADBifunctional protein PutA/0.446
4rqkATP3-phosphoinositide-dependent protein kinase 12.7.11.10.446
2b7aIZATyrosine-protein kinase JAK2/0.445
2g1n1IGRenin3.4.23.150.445
2x1nX1NCyclin-dependent kinase 22.7.11.220.445
3n6uTSUHTH-type transcriptional regulator TsaR/0.445
4aotGW8Serine/threonine-protein kinase 102.7.11.10.445
4eh9IRGMitogen-activated protein kinase 14/0.445
4fizCUE17beta-hydroxysteroid dehydrogenase/0.445
4fkr45KCyclin-dependent kinase 22.7.11.220.445
4jajXU1Aurora kinase A2.7.11.10.445
4l4dCAMCamphor 5-monooxygenase1.14.15.10.445
5cvhADPCasein kinase II subunit alpha2.7.11.10.445
5iqiGNPBifunctional AAC/APH2.3.10.445
1cerNADGlyceraldehyde-3-phosphate dehydrogenase/0.444
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.444
1h65GDPTranslocase of chloroplast 343.6.50.444
1msnJE2Gag-Pol polyprotein3.4.23.160.444
1q6t600Tyrosine-protein phosphatase non-receptor type 13.1.3.480.444
2cdz23DSerine/threonine-protein kinase PAK 42.7.11.10.444
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.444
3cisATPUniversal stress protein Rv2623/0.444
3r7eX88Cyclin-dependent kinase 22.7.11.220.444
3s79ASDAromatase1.14.14.140.444
3t8oATPRhodopsin kinase/0.444
3w0hW12Vitamin D3 receptor/0.444
3zbsOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.444
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.444
4xymCOAAcyl-CoA synthetase (NDP forming)/0.444
1eioGCHGastrotropin/0.443
1fxsNAPGDP-L-fucose synthase/0.443
1kfcIPLTryptophan synthase alpha chain/0.443
1powFADPyruvate oxidase1.2.3.30.443
1pr9NAPL-xylulose reductase1.1.1.100.443
1ykdCMPAdenylate cyclase/0.443
2e9n76ASerine/threonine-protein kinase Chk12.7.11.10.443
2j2pSC2Ficolin-2/0.443
2pvmP29Casein kinase II subunit alpha2.7.11.10.443
2pvnP63Casein kinase II subunit alpha2.7.11.10.443
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
2xvu9DNSerum albumin/0.443
3a14NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.443
3cd3STUTyrosine-protein kinase Fes/Fps2.7.10.20.443
3imgBZ2Pantothenate synthetase6.3.2.10.443
3tnwF18Cyclin-dependent kinase 22.7.11.220.443
4a83DXCMajor pollen allergen Bet v 1-A/0.443
4bibIEOMitogen-activated protein kinase kinase kinase 52.7.11.250.443
4cr8NADN-acylmannosamine 1-dehydrogenase1.1.1.2330.443
4d9t0JGRibosomal protein S6 kinase alpha-32.7.11.10.443
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.443
4q1y017Gag-Pol polyprotein3.4.23.160.443
4rrrA3TThreonine--tRNA ligase6.1.1.30.443
5kf9ACOPredicted acetyltransferase/0.443
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1gd1NADGlyceraldehyde-3-phosphate dehydrogenase/0.442
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1kquBR4Phospholipase A2, membrane associated/0.442
1pw6FRBInterleukin-2/0.442
1rfuADPPyridoxal kinase2.7.1.350.442
1txiTX5Vitamin D3 receptor/0.442
1u4oNDDL-lactate dehydrogenase1.1.1.270.442
1u8fNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.442
2briANPUridylate kinase2.7.4.220.442
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
2qhm7CSSerine/threonine-protein kinase Chk12.7.11.10.442
2w1fL0FAurora kinase A2.7.11.10.442
3gwfNAPCyclohexanone monooxygenase/0.442
3so9017Pol protein/0.442
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
4cgfUJ6Integrase/0.442
4hxyNDPPlm1/0.442
4l4eCAMCamphor 5-monooxygenase1.14.15.10.442
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
1dr3TAPDihydrofolate reductase1.5.1.30.441
1h74AGSHomoserine kinase2.7.1.390.441
1psa0ZLPepsin A3.4.23.10.441
1vyrFMNPentaerythritol tetranitrate reductase/0.441
2xnbY8LCyclin-dependent kinase 22.7.11.220.441
3b6zCO7Enoyl reductase LovC10.441
3eyhIZATyrosine-protein kinase JAK1/0.441
3gu83GUDeath-associated protein kinase 12.7.11.10.441
3hrfATP3-phosphoinositide-dependent protein kinase 12.7.11.10.441
3kb6NADD-lactate dehydrogenase/0.441
3mg3ECHOrange carotenoid-binding protein/0.441
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.441
3oafOAGDihydrofolate reductase1.5.1.30.441
3r83Z14Cyclin-dependent kinase 22.7.11.220.441
3vrwYS5Vitamin D3 receptor/0.441
3w0aDS5Vitamin D3 receptor/0.441
4b4dFADFerredoxin-NADP reductase/0.441
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
4fv5EK9Mitogen-activated protein kinase 12.7.11.240.441
4g2rH1LProbable propionyl-CoA carboxylase beta chain 66.4.1.30.441
4j491J1Uncharacterized protein/0.441
4lxhC1EAlpha/beta hydrolase fold/0.441
4o0rX4ZSerine/threonine-protein kinase PAK 12.7.11.10.441
4tuvCPZCytochrome P450 1191.140.441
5eccNAPDehydrofolate reductase type I/0.441
1a72PADAlcohol dehydrogenase E chain1.1.1.10.440
1b16NAQAlcohol dehydrogenase1.1.1.10.440
1nptNADGlyceraldehyde-3-phosphate dehydrogenase/0.440
1y57MPZProto-oncogene tyrosine-protein kinase Src2.7.10.20.440
1ydrIQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.440
3eksCY9Actin-5C/0.440
3q5dGDPAtlastin-13.6.50.440
3sw418KCyclin-dependent kinase 22.7.11.220.440
3vf80JETyrosine-protein kinase SYK2.7.10.20.440
3vt3VDXVitamin D3 receptor/0.440
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.440
4kl9NDPDihydrofolate reductase1.5.1.30.440
4otpADPSerine/threonine-protein kinase RIO12.7.11.10.440
4y8wSTRSteroid 21-hydroxylase/0.440