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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
4mv3ACPBiotin carboxylase6.3.4.14

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4mv3ACPBiotin carboxylase6.3.4.141.000
4mv1ADPBiotin carboxylase6.3.4.140.631
4mv4ACPBiotin carboxylase6.3.4.140.610
4mv8ACPBiotin carboxylase6.3.4.140.598
2v5aLZLBiotin carboxylase6.3.4.140.594
2j9gANPBiotin carboxylase6.3.4.140.587
2vr1ATFBiotin carboxylase6.3.4.140.587
2w6zL21Biotin carboxylase6.3.4.140.584
2w6qOA5Biotin carboxylase6.3.4.140.577
2w6oOA3Biotin carboxylase6.3.4.140.568
2v59LZKBiotin carboxylase6.3.4.140.545
2v58LZJBiotin carboxylase6.3.4.140.540
2w6mOA1Biotin carboxylase6.3.4.140.538
2w71L23Biotin carboxylase6.3.4.140.526
3jziJZLBiotin carboxylase6.3.4.140.516
2w6pOA4Biotin carboxylase6.3.4.140.508
2bf7HBIPteridine reductase 11.5.1.330.503
3jzfJZKBiotin carboxylase6.3.4.140.503
2hb7O1CVitamin D3 receptor/0.495
2j9gADPBiotin carboxylase6.3.4.140.495
2w6nOA2Biotin carboxylase6.3.4.140.483
4g8zTOPDihydrofolate reductase1.5.1.30.483
4h9753SDihydrofolate reductase1.5.1.30.483
1xddAAYIntegrin alpha-L/0.480
3lamKRPGag-Pol polyprotein2.7.7.490.480
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.479
2hasC3OVitamin D3 receptor/0.478
3h3r14HCollagen type IV alpha-3-binding protein/0.478
4rujVDXVitamin D3 receptor A/0.477
1e92HBIPteridine reductase 11.5.1.330.474
2hb8MVDVitamin D3 receptor/0.474
2xf3J01Uncharacterized protein/0.474
3ddw055Glycogen phosphorylase, liver form2.4.1.10.474
2zbaZBATrichothecene 3-O-acetyltransferase/0.473
2zl9VDAVitamin D3 receptor/0.473
3lfcZ86Mitogen-activated protein kinase 14/0.472
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.471
1rkhVD2Vitamin D3 receptor/0.470
1l8qADPChromosomal replication initiator protein DnaA/0.469
2vcmM11Isopenicillin N synthase1.21.3.10.469
2zlaVDBVitamin D3 receptor/0.469
3nj0PYVAbscisic acid receptor PYL2/0.469
4gk2L66Ephrin type-A receptor 32.7.10.10.469
3qls55VDihydrofolate reductase1.5.1.30.468
4f700STCyclin-dependent kinase 82.7.11.220.468
4iteTEYVitamin D3 receptor/0.468
4g1y0VOVitamin D3 receptor A/0.466
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.465
3eej53RUncharacterized protein/0.465
3nmpPYVAbscisic acid receptor PYL2/0.465
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.465
4ap1NAPSteroid monooxygenase/0.465
4g1d0VKVitamin D3 receptor A/0.465
4h9506UDihydrofolate reductase1.5.1.30.465
1ej2NADNicotinamide-nucleotide adenylyltransferase2.7.7.10.464
1osvCHCBile acid receptor/0.464
2zshGA3Gibberellin receptor GID1A30.464
3cseN22Uncharacterized protein/0.464
3kpzZNEVitamin D3 receptor/0.464
4ia1BIVVitamin D3 receptor A/0.464
1e7vLY2Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.463
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.463
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.463
2blaCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.463
1ie9VDXVitamin D3 receptor/0.462
2hamC33Vitamin D3 receptor/0.462
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.462
3gcq1BUMitogen-activated protein kinase 14/0.462
1oc1ASVIsopenicillin N synthase1.21.3.10.461
2iw6QQ2Cyclin-dependent kinase 22.7.11.220.461
3vt65YIVitamin D3 receptor/0.461
4fjyFJYPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.461
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.461
2fm0M98cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.460
2fwyH64Heat shock protein HSP 90-alpha/0.460
3eblGA4Gibberellin receptor GID1/0.460
3vrvYSDVitamin D3 receptor/0.460
3vrwYS5Vitamin D3 receptor/0.460
1y56FMNUncharacterized protein/0.459
1y56FMN382aa long hypothetical sarcosine oxidase/0.459
2w3wVG9Dihydrofolate reductase/0.459
3h3t16HCollagen type IV alpha-3-binding protein/0.459
3vrtYS2Vitamin D3 receptor/0.459
4u97STUInterleukin-1 receptor-associated kinase 42.7.11.10.459
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.459
1f5fDHTSex hormone-binding globulin/0.458
1j3jCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.458
2harOCCVitamin D3 receptor/0.458
2vbpVB1Isopenicillin N synthase1.21.3.10.458
2y6o1N1Ephrin type-A receptor 42.7.10.10.458
3lxiCAMCytochrome P450/0.458
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.458
4tzt468Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.458
1uy6PU3Heat shock protein HSP 90-alpha/0.457
2acwUPGGlycosyltransferase/0.457
2fszOHTEstrogen receptor beta/0.457
2jfaRALEstrogen receptor/0.457
1oynROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.456
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.456
2a5uQYTPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
2b365PPEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.456
2bfpH4BPteridine reductase 11.5.1.330.456
2fhnBNIAvidin-related protein 4/5/0.456
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.456
3h3sH15Collagen type IV alpha-3-binding protein/0.456
1cqp803Integrin alpha-L/0.455
1g2vTTPGlucose-1-phosphate thymidylyltransferase/0.455
1ie8KH1Vitamin D3 receptor/0.455
2bl9CP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.455
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.455
3tfq07MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.455
3vt5YI2Vitamin D3 receptor/0.455
3w0gW07Vitamin D3 receptor/0.455
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.455
1klkPMDDihydrofolate reductase1.5.1.30.454
1txiTX5Vitamin D3 receptor/0.454
1zknIBMcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
2k62ITLFatty acid-binding protein, liver/0.454
2x7hPFNProstaglandin reductase 310.454
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
3um5CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.454
4f6w0SSCyclin-dependent kinase 82.7.11.220.454
5jtbZMAAdenosine receptor A2a/0.454
2tpsTPSThiamine-phosphate synthase/0.453
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.453
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.453
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.453
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.453
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.453
1ot7CHCBile acid receptor/0.452
1s19MC9Vitamin D3 receptor/0.452
1upcTPPN(2)-(2-carboxyethyl)arginine synthase/0.452
3qg2CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.452
3sfuRBVPolyprotein/0.452
1n5vNOMActVA 6 protein/0.451
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.451
2lbaCHOFatty acid binding protein 6/0.451
2wo7ASVIsopenicillin N synthase1.21.3.10.451
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.451
3g58988cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
3h3qH13Collagen type IV alpha-3-binding protein/0.451
3h4vDVPPteridine reductase 11.5.1.330.451
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.451
4b95UCKVon Hippel-Lindau disease tumor suppressor/0.451
4q73FADBifunctional protein PutA/0.451
1i8tFADUDP-galactopyranose mutase5.4.99.90.450
1m78NDPDihydrofolate reductase1.5.1.30.450
1tojHCIAspartate aminotransferase2.6.1.10.450
1v35NAIEnoyl-ACP reductase/0.450
2aq8NAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
2rhrEMOPutative ketoacyl reductase1.3.10.450
3g493G4Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
3w5rLOAVitamin D3 receptor/0.450
4l8u9AZSerum albumin/0.450
1dg5TOPDihydrofolate reductase1.5.1.30.449
1t86CAMCamphor 5-monooxygenase1.14.15.10.449
2bfmTOPPteridine reductase 11.5.1.330.449
2gpuOHTEstrogen-related receptor gamma/0.449
2hcdBIVVitamin D3 receptor A/0.449
2vssACOHydroxycinnamoyl-CoA hydratase-lyase4.1.2.410.449
3lnbCOAN-acetyltransferase family protein/0.449
3w5tLHPVitamin D3 receptor/0.449
3zy6GFBGDP-fucose protein O-fucosyltransferase 12.4.1.2210.449
4eevL1XHepatocyte growth factor receptor2.7.10.10.449
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
4h9614QDihydrofolate reductase1.5.1.30.449
4l0qNADAlcohol dehydrogenase class-3/0.449
4q0a4OAVitamin D3 receptor A/0.449
5iu86DZAdenosine receptor A2a/0.449
5k2cZMAAdenosine receptor A2a/0.449
1fmjRTLRetinol dehydratase/0.448
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
1rx8FOLDihydrofolate reductase1.5.1.30.448
1unlRRCCyclin-dependent-like kinase 52.7.11.10.448
2bunFADAppA protein/0.448
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
2olcADPMethylthioribose kinase2.7.1.1000.448
2pvyACPFibroblast growth factor receptor 2/0.448
3cgeCOACoenzyme A disulfide reductase/0.448
3lq2TDPPyruvate dehydrogenase E1 component1.2.4.10.448
3qlrQLRDihydrofolate reductase1.5.1.30.448
3w0jT08Vitamin D3 receptor/0.448
4a51DQ8Kinesin-like protein KIF11/0.448
4fhj0TZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
3emlZMAAdenosine receptor A2a/0.448
1aoeGW3Dihydrofolate reductase1.5.1.30.447
1dhiMTXDihydrofolate reductase1.5.1.30.447
1dz6CAMCamphor 5-monooxygenase1.14.15.10.447
1g0rTHMGlucose-1-phosphate thymidylyltransferase/0.447
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
2apcUDMAlpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase2.4.1.1010.447
2c3kABOSerine/threonine-protein kinase Chk12.7.11.10.447
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.447
3e2sFADBifunctional protein PutA1.5.5.20.447
3oewNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.447
3sh25DRDihydrofolate reductase1.5.1.30.447
3w0aDS5Vitamin D3 receptor/0.447
4hh0FMNAppA protein/0.447
4trj665Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
1dr2TAPDihydrofolate reductase1.5.1.30.446
1pl8NADSorbitol dehydrogenase1.1.1.140.446
1rk3VDXVitamin D3 receptor/0.446
1uyhPU0Heat shock protein HSP 90-alpha/0.446
1yqj6NPMitogen-activated protein kinase 14/0.446
1z1fSTLResveratrol synthase/0.446
2c3u2TPPyruvate synthase/0.446
2qo9ANPEphrin type-A receptor 32.7.10.10.446
3bgiSAHThiopurine S-methyltransferase2.1.1.670.446
3cgdCOACoenzyme A disulfide reductase/0.446
3elm24FCollagenase 33.4.240.446
3gxoMQAMitomycin biosynthesis 6-O-methyltransferase/0.446
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.446
3wo0ADPAlanine--anticapsin ligase/0.446
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
4c3yANB3-ketosteroid dehydrogenase/0.446
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.446
4g1z0VPVitamin D3 receptor A/0.446
4rupH97Vitamin D3 receptor A/0.446
1eioGCHGastrotropin/0.445
1nvqUCNSerine/threonine-protein kinase Chk12.7.11.10.445
1xu9CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
2brmDFZSerine/threonine-protein kinase Chk12.7.11.10.445
2i40BLZCyclin-dependent kinase 22.7.11.220.445
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.445
2o8h227cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
2y67N21UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.445
3kb0A8SAbscisic acid receptor PYL2/0.445
3lovFADProtoporphyrinogen oxidase/0.445
3qf9NM8Serine/threonine-protein kinase pim-12.7.11.10.445
3vruYS3Vitamin D3 receptor/0.445
3vtcTK3Vitamin D3 receptor/0.445
3w0hW12Vitamin D3 receptor/0.445
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.445
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
1v0oINRCell division control protein 2 homolog2.7.11.220.444
2bxqIMNSerum albumin/0.444
2db3ANPATP-dependent RNA helicase vasa, isoform A3.6.4.130.444
2pmnK51Protein kinase 7/0.444
3l0lHC3Nuclear receptor ROR-gamma/0.444
3meeT27Gag-Pol polyprotein2.7.7.490.444
3oeyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
3otwCOAPhosphopantetheine adenylyltransferase/0.444
3pn1IVHDNA ligase/0.444
3q5dGDPAtlastin-13.6.50.444
4a83DXCMajor pollen allergen Bet v 1-A/0.444
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4gncASORegucalcin3.1.1.170.444
4l4xNDPAmphI/0.444
4nm9FADBifunctional protein PutA/0.444
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
5cccDDFDihydrofolate reductase1.5.1.30.444
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.444
5pahLDPPhenylalanine-4-hydroxylase1.14.16.10.444
7catNDPCatalase1.11.1.60.444
5k2aZMAAdenosine receptor A2a/0.444
1cbfSAHCobalt-precorrin-4 C(11)-methyltransferase2.1.1.2710.443
1equEQIEstradiol 17-beta-dehydrogenase 11.1.1.620.443
1g4tFTPThiamine-phosphate synthase/0.443
1pq6965Oxysterols receptor LXR-beta/0.443
1upw444Oxysterols receptor LXR-beta/0.443
1yrdCAMCamphor 5-monooxygenase1.14.15.10.443
2fr0NDP6-deoxyerythronolide-B synthase EryA1, modules 1 and 2/0.443
2ji9TPWOxalyl-CoA decarboxylase4.1.1.80.443
3c3dFO12-phospho-L-lactate transferase/0.443
3qfxCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
3rdqDTBStreptavidin/0.443
3s7a684Dihydrofolate reductase1.5.1.30.443
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
4bcqTJFCyclin-dependent kinase 22.7.11.220.443
4l1xSTRAldo-keto reductase family 1 member C2/0.443
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.443
4xivADPChemotaxis protein CheA2.7.13.30.443
5eccNAPDehydrofolate reductase type I/0.443
1b4pGPSGlutathione S-transferase Mu 2/0.442
1s9qOHTEstrogen-related receptor gamma/0.442
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.442
1vyw292Cyclin-dependent kinase 22.7.11.220.442
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
1zg32HIIsoflavone 4'-O-methyltransferase/0.442
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.442
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.442
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
3qlwN22Dihydrofolate reductase1.5.1.30.442
3to3ATPPetrobactin biosynthesis protein AsbB/0.442
3ukrCKHActin-related protein 3/0.442
3ukrCKHActin-related protein 2/0.442
4a86H35Major pollen allergen Bet v 1-A/0.442
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.442
4dtiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
4kne1CYDihydrofolate reductase1.5.1.30.442
3iogSDFMetallo-beta-lactamase type 2/0.441
3nr4PYVAbscisic acid receptor PYL2/0.441
3q7dNPXProstaglandin G/H synthase 21.14.99.10.441
3qpoPFRcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
4bis8HQLysine-specific demethylase 4A1.14.110.441
4o8aFADBifunctional protein PutA1.2.1.880.441
4ogrADNCyclin-dependent kinase 92.7.11.220.441
4pd6URINucleoside permease/0.441
4pk4ADPUnconventional myosin-VI/0.441
4q5jANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.441
1fvpFMANon-fluorescent flavoprotein/0.440
1piwNAPNADP-dependent alcohol dehydrogenase 61.1.1.20.440
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.440
1tl7FOKAdenylate cyclase type 2/0.440
1tl7FOKAdenylate cyclase type 5/0.440
2ad5ADPCTP synthase/0.440
2aqkNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
2cchATPCyclin-dependent kinase 22.7.11.220.440
2hl1A3SThreonine--tRNA ligase6.1.1.30.440
2i0y5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.440
2i5nUQ1Reaction center protein L chain/0.440
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.440
2zm1KSFTyrosine-protein kinase Lck2.7.10.20.440
3a783EVVitamin D3 receptor/0.440
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3fp0FP015-O-acetyltransferase/0.440
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3o0iP54Heat shock protein HSP 90-alpha/0.440
3vtbTKAVitamin D3 receptor/0.440
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4ia7BIVVitamin D3 receptor A/0.440
4imfSI3N-acetylneuraminate lyase/0.440
4inb1F6Gag protein/0.440
4py6R78Bromodomain protein, putative/0.440
4tzk641Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440