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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
3q5pTACMultidrug-efflux transporter 1 regulator

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3q5pTACMultidrug-efflux transporter 1 regulator/1.000
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.491
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.491
4mt92D6Tankyrase-12.4.2.300.484
5stdUNNScytalone dehydratase4.2.1.940.482
1ia1NDPDihydrofolate reductase1.5.1.30.480
1nenDNTSuccinate dehydrogenase iron-sulfur subunit1.3.5.10.479
1nenDNTSuccinate dehydrogenase cytochrome b556 subunit/0.479
2rqfJH3Hemolymph juvenile hormone binding protein/0.478
3ddw055Glycogen phosphorylase, liver form2.4.1.10.476
2cekN8TAcetylcholinesterase3.1.1.70.473
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.472
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.472
3nr4PYVAbscisic acid receptor PYL2/0.472
1t7o152Carnitine O-acetyltransferase2.3.1.70.471
3d84NDPDihydrofolate reductase1.5.1.30.471
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.471
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.471
5bt42LOBromodomain-containing protein 4/0.471
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.470
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.469
4a83DXCMajor pollen allergen Bet v 1-A/0.469
4iaq2GM5-hydroxytryptamine receptor 1B/0.469
3nxxNDPDihydrofolate reductase1.5.1.30.468
4xwtU5PRibonuclease J/0.468
1rszDIHPurine nucleoside phosphorylase2.4.2.10.467
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
1dliUDXUDP-glucose 6-dehydrogenase/0.466
4esoNAPPutative oxidoreductase/0.466
2gjlFMNNitronate monooxygenase1.13.12.160.465
2op18PCEnoyl-ACP reductase/0.465
3drcMTXDihydrofolate reductase1.5.1.30.465
1pd9CO4Dihydrofolate reductase1.5.1.30.464
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.464
3zv7NHGAcetylcholinesterase3.1.1.70.464
5cc9DDFDihydrofolate reductase1.5.1.30.464
1dhiMTXDihydrofolate reductase1.5.1.30.463
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.462
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.461
1zx1CB1Ribosyldihydronicotinamide dehydrogenase [quinone]/0.461
4b67NAPL-ornithine N(5)-monooxygenase/0.461
4iyg1HUStrictosidine synthase4.3.3.20.461
4tjy3GNTankyrase-22.4.2.300.461
1fm4DXCMajor pollen allergen Bet v 1-L/0.460
1mlzPLPAdenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.460
1sreHABStreptavidin/0.460
2nnqT4BFatty acid-binding protein, adipocyte/0.460
3nj0PYVAbscisic acid receptor PYL2/0.460
3ns2PYVAbscisic acid receptor PYL2/0.460
1lkdBP6Biphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.459
1m52P17Tyrosine-protein kinase ABL12.7.10.20.459
3ggs2FDPurine nucleoside phosphorylase2.4.2.10.459
4bj9UHBTankyrase-22.4.2.300.459
4fam0SZAldo-keto reductase family 1 member C3/0.459
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
1dljUGAUDP-glucose 6-dehydrogenase/0.458
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.458
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.458
2v13C40Renin3.4.23.150.458
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3ntz3TZDihydrofolate reductase1.5.1.30.458
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.458
1dr3HBIDihydrofolate reductase1.5.1.30.457
1o5rFR9Adenosine deaminase3.5.4.40.457
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.457
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.457
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.457
3dd125DGlycogen phosphorylase, liver form2.4.1.10.457
3oafOAGDihydrofolate reductase1.5.1.30.457
3qbwADPAnhydro-N-acetylmuramic acid kinase/0.457
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.457
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.457
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.457
4mr61K0Bromodomain-containing protein 2/0.457
1hfqMOTDihydrofolate reductase1.5.1.30.456
1osvCHCBile acid receptor/0.456
2fpcSCGStrictosidine synthase4.3.3.20.456
1b2lNDCAlcohol dehydrogenase1.1.1.10.455
1m78NDPDihydrofolate reductase1.5.1.30.455
1me6IVSPlasmepsin-23.4.23.390.455
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.455
1w4lGL8Acetylcholinesterase3.1.1.70.455
3bxoUPPdTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose/0.455
3p67FMNPentaerythritol tetranitrate reductase/0.455
3up0D7SaceDAF-12/0.455
4bfyZVYPantothenate kinase2.7.1.330.455
4m6l21VDihydrofolate reductase1.5.1.30.455
2xuiTZ5Acetylcholinesterase3.1.1.70.454
3bgsDIHPurine nucleoside phosphorylase2.4.2.10.454
3c6tM14Gag-Pol polyprotein2.7.7.490.454
3qiyQI1Botulinum neurotoxin type A3.4.24.690.454
3r43ID8Aldo-keto reductase family 1 member C3/0.454
3dmjGWEPol protein/0.453
1ai9NDPDihydrofolate reductase1.5.1.30.452
1fmlRTLRetinol dehydratase/0.452
1kp2ATPArgininosuccinate synthase6.3.4.50.452
1opbRETRetinol-binding protein 2/0.452
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.452
3b9xNOSPyrimidine-specific ribonucleoside hydrolase RihB3.2.2.80.452
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3o4rNAPDehydrogenase/reductase SDR family member 41.1.1.1840.452
3o73O73Ribosyldihydronicotinamide dehydrogenase [quinone]/0.452
3ufl508Beta-secretase 13.4.23.460.452
1mvtDTMDihydrofolate reductase1.5.1.30.451
1s3uTQDDihydrofolate reductase1.5.1.30.451
1z6tADPApoptotic protease-activating factor 1/0.451
2aclREARetinoic acid receptor RXR-alpha/0.451
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.451
3djfBC3Purine nucleoside phosphorylase/0.451
3dleGFAGag-Pol polyprotein2.7.7.490.451
3zeiAWHO-acetylserine sulfhydrylase/0.451
4b45GSPTubulin-like protein CetZ2/0.451
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
4l0qNADAlcohol dehydrogenase class-3/0.451
1qxlFR8Adenosine deaminase3.5.4.40.450
1ry0PG2Aldo-keto reductase family 1 member C3/0.450
2bxqIMNSerum albumin/0.450
3frkTQPQdtB/0.450
4at0FADPossible succinate dehydrogenase/0.450
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.450
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.450
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.450
1ay0TPPTransketolase 12.2.1.10.449
1dr3TAPDihydrofolate reductase1.5.1.30.449
1nsgRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.449
1nsgRADSerine/threonine-protein kinase mTOR2.7.11.10.449
1pz1NAPGeneral stress protein 69/0.449
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.449
3lakKR1Gag-Pol polyprotein2.7.7.490.449
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.448
1tbbROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
2a0wDIHPurine nucleoside phosphorylase2.4.2.10.448
2bu9HFVIsopenicillin N synthase1.21.3.10.448
2hw2RFPRifampin ADP-ribosyl transferase/0.448
2r6jNDPEugenol synthase 11.1.1.3180.448
1bozPRDDihydrofolate reductase1.5.1.30.447
1qtiGNTAcetylcholinesterase3.1.1.70.447
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.447
3nhjA2ZRibosyldihydronicotinamide dehydrogenase [quinone]/0.447
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4g8zTOPDihydrofolate reductase1.5.1.30.447
4g95OAGDihydrofolate reductase1.5.1.30.447
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.447
4zm6ACON-acetyl-beta-D glucosaminidase/0.447
1dkfBMSRetinoic acid receptor alpha/0.446
1jlaTNKGag-Pol polyprotein2.7.7.490.446
1ppjANYCytochrome b/0.446
2amb17HAndrogen receptor/0.446
2qboCAMCamphor 5-monooxygenase1.14.15.10.446
2vcmM11Isopenicillin N synthase1.21.3.10.446
3b5iSAHIndole-3-acetate O-methyltransferase 1/0.446
3dds26BGlycogen phosphorylase, liver form2.4.1.10.446
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.446
3hv3R49Mitogen-activated protein kinase 14/0.446
3sfxJANUncharacterized protein/0.446
3v2uATPProtein GAL3/0.446
4a84DXCMajor pollen allergen Bet v 1-A/0.446
4jlj1NMDeoxycytidine kinase2.7.1.740.446
1j3jCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.445
1s3yTQTDihydrofolate reductase1.5.1.30.445
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
2a0yDIHPurine nucleoside phosphorylase2.4.2.10.445
2b36NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
2vssACOHydroxycinnamoyl-CoA hydratase-lyase4.1.2.410.445
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
4i9i1DYTankyrase-12.4.2.300.445
1mvsDTMDihydrofolate reductase1.5.1.30.444
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.444
2p1v5TNRetinoic acid receptor RXR-alpha/0.444
3c6uM22Gag-Pol polyprotein2.7.7.490.444
3dg8RJ6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.444
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3fu83DMLaccase-11.10.3.20.444
3nmpPYVAbscisic acid receptor PYL2/0.444
4hmn16JAldo-keto reductase family 1 member C3/0.444
4jvnYUGEstrogen sulfotransferase2.8.2.40.444
1enpNADEnoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic1.3.1.90.443
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.443
1iayAVG1-aminocyclopropane-1-carboxylate synthase 24.4.1.140.443
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
2ea1GPGRibonuclease I3.1.27.60.443
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.443
3jpuTY4Transcriptional activator protein LasR/0.443
3ov4EQUSteroid Delta-isomerase5.3.3.10.443
3zhbNAPPutative dehydrogenase/0.443
4kw51W6Decaprenylphosphoryl-beta-D-ribose oxidase/0.443
1diuBDMDihydrofolate reductase1.5.1.30.442
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.442
1g3mPCQEstrogen sulfotransferase2.8.2.40.442
1itzTPPTransketolase, chloroplastic2.2.1.10.442
1kceCB3Thymidylate synthase/0.442
1obnASVIsopenicillin N synthase1.21.3.10.442
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
2be2R22Gag-Pol polyprotein2.7.7.490.442
3caqNDP3-oxo-5-beta-steroid 4-dehydrogenase/0.442
3cseN22Uncharacterized protein/0.442
3fktSIIBeta-secretase 13.4.23.460.442
3gu3SAHMethyltransferase/0.442
4ajwVWNPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform2.7.1.1530.442
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4psbGA3Cytokinin-specific binding protein/0.442
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.442
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.442
5h8tRTLRetinol-binding protein 1/0.442
1qjgEQUSteroid Delta-isomerase5.3.3.10.441
2jkcFADFlavin-dependent tryptophan halogenase PrnA1.14.19.90.441
2mm3CHOGastrotropin/0.441
2rhrEMOPutative ketoacyl reductase1.3.10.441
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.441
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3gwfFADCyclohexanone monooxygenase/0.441
3gwfNAPCyclohexanone monooxygenase/0.441
3rtnRTNBeta-secretase 13.4.23.460.441
3s3vTOPDihydrofolate reductase1.5.1.30.441
3v1s0LHStrictosidine synthase4.3.3.20.441
4bb3KKAIsopenicillin N synthase1.21.3.10.441
4ckrDI1Epithelial discoidin domain-containing receptor 12.7.10.10.441
4wx2F6FTryptophan synthase alpha chain/0.441
4wx2F6FTryptophan synthase beta chain4.2.1.200.441
1hvyD16Thymidylate synthase2.1.1.450.440
1pq6965Oxysterols receptor LXR-beta/0.440
1q13TESProstaglandin-E(2) 9-reductase1.1.1.1890.440
1rt1MKCGag-Pol polyprotein2.7.7.490.440
1s19MC9Vitamin D3 receptor/0.440
1x7hNDPPutative ketoacyl reductase1.3.10.440
1xduSFGAclacinomycin 10-hydroxylase RdmB4.1.10.440
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
2vprTDCTetracycline repressor protein class H/0.440
2w3wVG9Dihydrofolate reductase/0.440
2w6cBM4Acetylcholinesterase3.1.1.70.440
2zi53L1Deoxycytidine kinase2.7.1.740.440
3b9lAZZSerum albumin/0.440
3k7mFAD6-hydroxy-L-nicotine oxidase/0.440
3pm1ETHTH-type transcriptional regulator QacR/0.440
3zkuHCVIsopenicillin N synthase1.21.3.10.440
4b66NAPL-ornithine N(5)-monooxygenase/0.440
5d7pOCZNAD-dependent protein deacetylase sirtuin-23.5.10.440