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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
4mrxCZHObelin

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4mrxCZHObelin/1.000
4n1fCZHObelin/0.681
1qv0CZHObelin/0.656
1el4CTZObelin/0.633
1jf2CZHObelin/0.626
1qv1CZHObelin/0.618
1jf0CZHObelin/0.614
1uhhCZPAequorin-2/0.601
1s36CEIObelin/0.599
1ej3CZHAequorin-2/0.594
4nqgCZHMitrocomin/0.555
2f3815MAldo-keto reductase family 1 member C3/0.541
2d06ESTSulfotransferase 1A12.8.2.10.515
1gt5BZQOdorant-binding protein/0.506
1ry0PG2Aldo-keto reductase family 1 member C3/0.505
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.505
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.504
4fa30SLAldo-keto reductase family 1 member C3/0.504
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.498
1ah3TOLAldose reductase1.1.1.210.492
4dbw511Aldo-keto reductase family 1 member C3/0.489
1zq5E04Aldo-keto reductase family 1 member C3/0.488
4h7c10HAldo-keto reductase family 1 member C3/0.488
5cc9DDFDihydrofolate reductase1.5.1.30.488
3hbfMYCFlavonoid 3-O-glucosyltransferase2.4.10.487
3r6iJMSAldo-keto reductase family 1 member C3/0.487
1ro6ROLcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.486
2pdh47DAldose reductase1.1.1.210.486
4kbn25UDihydrofolate reductase1.5.1.30.486
3o9lLPNRenin3.4.23.150.485
4u95MIYMultidrug efflux pump subunit AcrB/0.485
3fu83DMLaccase-11.10.3.20.484
3g58988cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.484
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.484
4eilFOLBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.484
4ky404JBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.484
3cth319Hepatocyte growth factor receptor2.7.10.10.483
4n4t2GVTankyrase-12.4.2.300.483
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.482
2f98NGVAklanonic acid methyl ester cyclase AcmA5.5.1.230.481
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.481
2c1zKMPAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.480
3hywDCQSulfide-quinone reductase/0.480
4fal0T0Aldo-keto reductase family 1 member C3/0.479
1ry8RUTAldo-keto reductase family 1 member C3/0.478
2c1zU2FAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.478
3hthPRLEbrA repressor/0.478
2pdfZSTAldose reductase1.1.1.210.477
3ug8IMNAldo-keto reductase family 1 member C3/0.476
3sl6JN8cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.475
3up3XCAaceDAF-12/0.475
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.474
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.474
2pdlTOLAldose reductase1.1.1.210.474
3nxrD2DDihydrofolate reductase1.5.1.30.474
3ugrIMNAldo-keto reductase family 1 member C3/0.474
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.474
4hmn16JAldo-keto reductase family 1 member C3/0.474
4pnrG18Tankyrase-22.4.2.300.474
2g7yMO9Cathepsin S3.4.22.270.473
2qw8NAPEugenol synthase 11.1.1.3180.473
3htjETEbrA repressor/0.473
3l71AZOCytochrome b/0.473
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.473
1o6qR17Squalene--hopene cyclase4.2.1.1290.472
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.472
3r8hZOMAldo-keto reductase family 1 member C3/0.472
2is72CLAldose reductase1.1.1.210.471
2vz0D64Pteridine reductase/0.471
4jpg1OXPyruvate kinase PKM2.7.1.400.471
5ctoNTD4-hydroxyphenylpyruvate dioxygenase1.13.11.270.471
1sjwNGVNogalonic acid methyl ester cyclase/0.470
1z4iUMP5'(3')-deoxyribonucleotidase, mitochondrial3.1.30.470
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.470
4li61XOTankyrase-12.4.2.300.470
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.469
2vcgS17Histone deacetylase-like amidohydrolase3.5.10.469
2yhuWHFPteridine reductase/0.469
4dbuBT9Aldo-keto reductase family 1 member C3/0.469
4hutATPCob(I)yrinic acid a,c-diamide adenosyltransferase2.5.1.170.469
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.468
3ghvGHCDihydrofolate reductase1.5.1.30.468
3o56ZG1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.468
4kykIMNLactoylglutathione lyase4.4.1.50.468
1ohkCOPDihydrofolate reductase1.5.1.30.467
1oynROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.467
1tbbROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.467
3p9tTCLRepressor/0.467
3uzcT4EAdenosine receptor A2a/0.467
3emlZMAAdenosine receptor A2a/0.467
4dbs0HVAldo-keto reductase family 1 member C3/0.466
1xngDNDNH(3)-dependent NAD(+) synthetase6.3.1.50.465
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.465
3o57ZG2cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.465
3bmnAX3Pteridine reductase/0.464
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.464
4pnmNU1Tankyrase-22.4.2.300.464
3gncQQQGlutaryl-CoA dehydrogenase/0.463
3pz23PZGeranylgeranyl transferase type-2 subunit beta2.5.1.600.463
3r43ID8Aldo-keto reductase family 1 member C3/0.463
4kak06UDihydrofolate reductase1.5.1.30.463
3hxeBD8Geranylgeranyl transferase type-2 subunit beta2.5.1.600.462
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.461
2bxoOPBSerum albumin/0.461
2psjCEIRenilla-luciferin 2-monooxygenase1.13.12.50.461
3sfh1DIHistone deacetylase 83.5.1.980.461
1yc2NADNAD-dependent protein deacylase 2/0.460
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.460
2fzbTOLAldose reductase1.1.1.210.460
3aiqHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic3.2.1.1820.460
3l6jZ90Alr2278 protein/0.460
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
3njoPYVAbscisic acid receptor PYR1/0.460
4i9i1DYTankyrase-12.4.2.300.460
1o6rR19Squalene--hopene cyclase4.2.1.1290.459
1vkgCRIHistone deacetylase 83.5.1.980.459
1x1aSAMC-20 methyltransferase/0.459
2bktRPFRenin3.4.23.150.459
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.459
2acwUPGGlycosyltransferase/0.458
2dv0ZSTAldose reductase1.1.1.210.458
3jq8DX3Pteridine reductase, putative/0.458
4dm6TTBRetinoic acid receptor beta/0.458
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.458
1frbZSTAldose reductase-related protein 2/0.457
3f0rTSNHistone deacetylase 83.5.1.980.457
3g4lROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.457
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.457
3n0hTOPDihydrofolate reductase1.5.1.30.457
1ro98BRcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.456
1tg56454-hydroxyphenylpyruvate dioxygenase1.13.11.270.456
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.456
2bjsACVIsopenicillin N synthase1.21.3.10.456
2qjpANJCytochrome b/0.456
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.456
3t37FADPyridoxine 4-oxidase/0.456
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.456
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.455
1yhoTRRDihydrofolate reductase1.5.1.30.455
2ipjFFAAldo-keto reductase family 1 member C2/0.455
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.455
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.455
4fam0SZAldo-keto reductase family 1 member C3/0.455
4jvlESTEstrogen sulfotransferase2.8.2.40.455
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.454
1w6jR71Lanosterol synthase5.4.99.70.454
2zb8IMNProstaglandin reductase 21.3.1.480.454
3h3r14HCollagen type IV alpha-3-binding protein/0.454
3r7mSUZAldo-keto reductase family 1 member C3/0.454
4jvmXDIEstrogen sulfotransferase2.8.2.40.454
1mlzPLPAdenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.453
2o8h227cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
2ovvPFHcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
2y0jAXCcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
3gyf51PDihydrofolate reductase1.5.1.30.453
3zg6APRNAD-dependent protein deacetylase sirtuin-63.5.10.453
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
4fcd0T6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
4gqkADPActin cross-linking toxin VgrG1/0.453
4k4eK4ETankyrase-12.4.2.300.453
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
2fs4PZ1Renin3.4.23.150.452
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
3r94FLRAldo-keto reductase family 1 member C3/0.452
4ea2RWZDehydrosqualene synthase/0.452
4imoPWZProstaglandin-H2 D-isomerase5.3.99.20.452
1hfrMOTDihydrofolate reductase1.5.1.30.451
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.451
2rqfJH3Hemolymph juvenile hormone binding protein/0.451
2x9vTMQPteridine reductase/0.451
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
3t31DCQSulfide-quinone reductase/0.451
3vjcZGASqualene synthase2.5.1.210.451
3wavDWVEctonucleotide pyrophosphatase/phosphodiesterase family member 23.1.4.390.451
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
4bfyZVYPantothenate kinase2.7.1.330.451
4dz5NAPAldo-keto reductase family 1 member C3/0.451
4lm4JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
4xo7ASDAldo-keto reductase family 1 member C2/0.451
2fzjDH3Dihydrofolate reductase1.5.1.30.450
3fnu006HAP protein/0.450
3iiuPIDPeridinin-chlorophyll a-binding protein 1, chloroplastic/0.450
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
1xf0ASDAldo-keto reductase family 1 member C3/0.449
2x9gLYAPteridine reductase/0.449
3jt4H4BNitric oxide synthase, brain1.14.13.390.449
3oq13OQCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.449
3tvxPNXcAMP-specific 3',5'-cyclic phosphodiesterase 4A3.1.4.530.449
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.449
4hqvQEIQueuine tRNA-ribosyltransferase2.4.2.290.449
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.449
1dlrMXADihydrofolate reductase1.5.1.30.448
1e2lTMCThymidine kinase/0.448
1pd8CO4Dihydrofolate reductase1.5.1.30.448
1t47NTD4-hydroxyphenylpyruvate dioxygenase1.13.11.270.448
2fq6P3FCystathionine beta-lyase MetC4.4.1.80.448
2qx7NAPEugenol synthase 11.1.1.3180.448
2w3aTOPDihydrofolate reductase1.5.1.30.448
2zevIPEGeranylgeranyl pyrophosphate synthase/0.448
2zozETTranscriptional regulator/0.448
3gi2GHWDihydrofolate reductase1.5.1.30.448
3h3t16HCollagen type IV alpha-3-binding protein/0.448
3hx3RETRetinaldehyde-binding protein 1/0.448
3nxtD2EDihydrofolate reductase1.5.1.30.448
3rsv3RSBeta-secretase 13.4.23.460.448
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.448
4nbiD3YD-tyrosyl-tRNA(Tyr) deacylase/0.448
1ly4COQDihydrofolate reductase1.5.1.30.447
1rpwDIDHTH-type transcriptional regulator QacR/0.447
1s07PLPAdenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.447
1swgBTNStreptavidin/0.447
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
2xuiTZ5Acetylcholinesterase3.1.1.70.447
2zitNADExotoxin A2.4.2.360.447
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.447
3r8gIZPAldo-keto reductase family 1 member C3/0.447
3t0kDCQSulfide-quinone reductase/0.447
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.447
4iah1DXAlr2278 protein/0.447
1fmjRTLRetinol dehydratase/0.446
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
2cbqTH2Neocarzinostatin/0.446
2yiuSMACytochrome b/0.446
3gieACPSensor histidine kinase DesK2.7.13.30.446
3r58NPSAldo-keto reductase family 1 member C3/0.446
4bfwZVWPantothenate kinase2.7.1.330.446
4e0u0MVCyclic dipeptide N-prenyltransferase/0.446
4pv5CBWLactoylglutathione lyase4.4.1.50.446
1dr4HBIDihydrofolate reductase1.5.1.30.445
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.445
1q9mROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
1zgcA2EAcetylcholinesterase3.1.1.70.445
2aotSAHHistamine N-methyltransferase2.1.1.80.445
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.445
2hzqSTRApolipoprotein D/0.445
4li71XPTankyrase-12.4.2.300.445
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.445
5stdUNNScytalone dehydratase4.2.1.940.445
1k8zIAGTryptophan synthase alpha chain/0.444
1t41ID5Aldose reductase1.1.1.210.444
1u72MTXDihydrofolate reductase1.5.1.30.444
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
2g263LGRenin3.4.23.150.444
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.444
3dkoIHZEphrin type-A receptor 72.7.10.10.444
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
3h4vDVPPteridine reductase 11.5.1.330.444
3k4551PDihydrofolate reductase1.5.1.30.444
3ox279XRibosyldihydronicotinamide dehydrogenase [quinone]/0.444
3t8xT8XT-cell surface glycoprotein CD1b/0.444
4kebFOLDihydrofolate reductase1.5.1.30.444
4wljIK2Kynurenine--oxoglutarate transaminase 12.6.1.70.444
1drfFOLDihydrofolate reductase1.5.1.30.443
1fcy564Retinoic acid receptor gamma/0.443
1gpnHUBAcetylcholinesterase3.1.1.70.443
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
1tfz8694-hydroxyphenylpyruvate dioxygenase1.13.11.270.443
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.443
2aouCQAHistamine N-methyltransferase2.1.1.80.443
2cekN8TAcetylcholinesterase3.1.1.70.443
3lakKR1Gag-Pol polyprotein2.7.7.490.443
3mauPLRPutative sphingosine-1-phosphate lyase/0.443
1s2cFLFAldo-keto reductase family 1 member C3/0.442
1ygjRMCPyridoxal kinase2.7.1.350.442
1zgbA1EAcetylcholinesterase3.1.1.70.442
2gvcFADThiol-specific monooxygenase1.14.130.442
2h7jH7JCathepsin S3.4.22.270.442
2r6jNDPEugenol synthase 11.1.1.3180.442
2vbvFMNRiboflavin kinase2.7.1.1610.442
2xi4AFTAcetylcholinesterase3.1.1.70.442
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3szfDCQSulfide-quinone reductase/0.442
4dm8REARetinoic acid receptor beta/0.442
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4klaCHDFerrochelatase, mitochondrial4.99.1.10.442
5k8bPDG8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase/0.442
1h35R01Squalene--hopene cyclase4.2.1.1290.441
1s7gNADNAD-dependent protein deacylase 2/0.441
1u65CP0Acetylcholinesterase3.1.1.70.441
2g274LGRenin3.4.23.150.441
2mm3CHOGastrotropin/0.441
3jq6DX1Pteridine reductase, putative/0.441
3nosH4BNitric oxide synthase, endothelial1.14.13.390.441
3tkyN7I(Iso)eugenol O-methyltransferase2.1.1.1460.441
4dvi2IWTankyrase-12.4.2.300.441
4iae1DXAlr2278 protein/0.441
4stdBFSScytalone dehydratase4.2.1.940.441
1ddtAPUDiphtheria toxin/0.440
1pj7FFODimethylglycine oxidase1.5.3.100.440
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.440
1rtiHEFGag-Pol polyprotein2.7.7.490.440
1z8962PAldose reductase1.1.1.210.440
2ejuSAHtRNA (guanine(26)-N(2))-dimethyltransferase/0.440
3jq9AX1Pteridine reductase, putative/0.440
3jt3H4BNitric oxide synthase, brain1.14.13.390.440
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3rgzBLDProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.440
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4e70N7IConiferyl alcohol 9-O-methyltransferase/0.440
4jq3ZOMAldo-keto reductase family 1 member C2/0.440
4mm48PRNa(+):neurotransmitter symporter (Snf family)/0.440