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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
3d77NBBPheromone-binding protein ASP1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3d77NBBPheromone-binding protein ASP1/1.000
3d75NBBPheromone-binding protein ASP1/0.618
3bfa9ODOdorant binding protein ASP1/0.588
3bfb9ODPheromone-binding protein ASP1/0.568
3d76NBBPheromone-binding protein ASP1/0.563
3d74NBBPheromone-binding protein ASP1/0.545
4nb6444Nuclear receptor ROR-gamma/0.508
3d73NBBPheromone-binding protein ASP1/0.501
3bjhNBBOdorant binding protein ASP1/0.500
4caxMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.495
1fp1HCCIsoliquiritigenin 2'-O-methyltransferase/0.494
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.487
3reyXACAdenosine receptor A2a/0.486
2hk9NAPShikimate dehydrogenase (NADP(+))/0.482
3d78NBBPheromone-binding protein ASP1/0.479
1xddAAYIntegrin alpha-L/0.478
2po7CHDFerrochelatase, mitochondrial4.99.1.10.477
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.476
4mt92D6Tankyrase-12.4.2.300.473
1iyzNDPProbable quinone oxidoreductase/0.472
2vbpVB1Isopenicillin N synthase1.21.3.10.471
3a1l2CCCytochrome P450/0.471
3qppPFWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.471
4ia3BIVVitamin D3 receptor A/0.471
3wy0COAUncharacterized protein/0.470
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.469
3ctj320Hepatocyte growth factor receptor2.7.10.10.469
3wxyCOAUncharacterized protein/0.469
2y6fM9FIsopenicillin N synthase1.21.3.10.468
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.468
3t8xT8XT-cell surface glycoprotein CD1b/0.468
3uzaT4GAdenosine receptor A2a/0.468
1oc1ASVIsopenicillin N synthase1.21.3.10.467
1w06W05Isopenicillin N synthase1.21.3.10.467
4dvi2IWTankyrase-12.4.2.300.467
4fnyI3KALK tyrosine kinase receptor2.7.10.10.467
1kkq471Peroxisome proliferator-activated receptor alpha/0.466
1r2jFADFkbI/0.466
3vt5YI2Vitamin D3 receptor/0.466
4l8u9AZSerum albumin/0.466
4n4v2GYTankyrase-12.4.2.300.466
4ea30NNNociceptin receptor/0.466
2lbvEB4Extracellular fatty acid-binding protein/0.465
3abaFLICytochrome P450/0.465
3kpzZNEVitamin D3 receptor/0.465
1zidZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.464
4nkvAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.464
3rfmCFFAdenosine receptor A2a/0.464
2pnuENMAndrogen receptor/0.463
2vcmM11Isopenicillin N synthase1.21.3.10.463
3w1wCHDFerrochelatase, mitochondrial4.99.1.10.463
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.462
1fmjRTLRetinol dehydratase/0.462
2zl9VDAVitamin D3 receptor/0.462
4myq19TcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.462
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.462
1ly4COQDihydrofolate reductase1.5.1.30.461
2qjpANJCytochrome b/0.461
2r0pK2CPutative FAD-monooxygenase/0.461
3tm5SFGUncharacterized protein/0.461
4eevL1XHepatocyte growth factor receptor2.7.10.10.461
4h380YXDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.461
3emlZMAAdenosine receptor A2a/0.461
1db1VDXVitamin D3 receptor/0.460
3ogqAB1Pol polyprotein/0.460
3p6pA6BCamphor 5-monooxygenase1.14.15.10.460
4j6cSTRCytochrome P450 monooxygenase/0.460
4jqh1MFAlr2278 protein/0.460
2hm9TRRDihydrofolate reductase1.5.1.30.459
2y60M8FIsopenicillin N synthase1.21.3.10.459
4b4w9L9Bifunctional protein FolD/0.459
5k2bZMAAdenosine receptor A2a/0.459
3vt7VDXVitamin D3 receptor/0.458
4b1fKRHGlutamate racemase/0.458
4c1iEH9cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.458
3ce31FNHepatocyte growth factor receptor2.7.10.10.457
3hcrCHDFerrochelatase, mitochondrial4.99.1.10.457
3iisPIDPeridinin-chlorophyll a-binding protein 1, chloroplastic/0.457
4b4vL34Bifunctional protein FolD/0.457
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.457
4h4o506Gag-Pol polyprotein2.7.7.490.457
4ri1ACOUDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase2.3.1.2020.457
5fm7ADPRuvB-like helicase/0.457
3bgiSAHThiopurine S-methyltransferase2.1.1.670.456
4msg2C6Tankyrase-12.4.2.300.456
5jadFB2Platelet-activating factor acetylhydrolase3.1.1.470.456
1kyoSMACytochrome b/0.455
1rdtL79Retinoic acid receptor RXR-alpha/0.455
3l8sBFFMitogen-activated protein kinase 14/0.455
3mdmFJZCholesterol 24-hydroxylase/0.455
3p6mDSOCamphor 5-monooxygenase1.14.15.10.455
3thrC2FGlycine N-methyltransferase2.1.1.200.455
4uyaAGSMitogen-activated protein kinase kinase kinase 212.7.11.250.455
2dw4FADLysine-specific histone demethylase 1A10.454
2fpcSCGStrictosidine synthase4.3.3.20.454
2fziDH3Dihydrofolate reductase1.5.1.30.454
2ntjP1HEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
4u2lSFDCholesterol oxidase1.1.3.60.454
1kzjCB3Thymidylate synthase/0.453
2uxoTACHTH-type transcriptional regulator TtgR/0.453
2wd8VGFPteridine reductase/0.453
2wpxACOOrf14/0.453
3qpnPFKcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
4ia1BIVVitamin D3 receptor A/0.453
4n4t2GVTankyrase-12.4.2.300.453
5bp9SAHPutative methyltransferase protein/0.453
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.453
1tbbROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
1zgaHMKIsoflavone 4'-O-methyltransferase/0.452
2h42VIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.452
2jn3JN3Fatty acid-binding protein, liver/0.452
2x21PIDPeridinin-chlorophyll a-binding protein 1, chloroplastic/0.452
2zlcVDXVitamin D3 receptor/0.452
3ipq965Oxysterols receptor LXR-alpha/0.452
3oq13OQCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
3t113T1Gag-Pol polyprotein3.4.23.160.452
3vtdTKDVitamin D3 receptor/0.452
4heu15JcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
5k2dZMAAdenosine receptor A2a/0.452
1vkgCRIHistone deacetylase 83.5.1.980.451
1x8lOXRRetinol dehydratase/0.451
1y4lSVRBasic phospholipase A2 homolog 2/0.451
2ij7TPFMycocyclosin synthase1.14.21.90.451
2x7hPFNProstaglandin reductase 310.451
2z3uCRRCytochrome P450/0.451
3vtbTKAVitamin D3 receptor/0.451
4iarERM5-hydroxytryptamine receptor 1B/0.451
4muw2F4cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
3uzcT4EAdenosine receptor A2a/0.451
1osvCHCBile acid receptor/0.450
1wuuANPGalactokinase2.7.1.60.450
2znnS44Peroxisome proliferator-activated receptor alpha/0.450
3zoiM2WIsopenicillin N synthase1.21.3.10.450
4elg52JDihydrofolate reductase/0.450
4g1y0VOVitamin D3 receptor A/0.450
4j6bPLOCytochrome P450 monooxygenase/0.450
5jtbZMAAdenosine receptor A2a/0.450
2bu9HFVIsopenicillin N synthase1.21.3.10.449
2c7xNRBCytochrome P450 monooxygenase PikC/0.449
2e0nSAHPrecorrin-2 C20-methyltransferase/0.449
3eta351Insulin receptor2.7.10.10.449
3fkoFKOMitogen-activated protein kinase 14/0.449
3njoPYVAbscisic acid receptor PYR1/0.449
3p3zP3ZPutative cytochrome P450/0.449
3q3cNADNAD-dependent L-serine dehydrogenase/0.449
3qly55VUncharacterized protein/0.449
3tkyN7I(Iso)eugenol O-methyltransferase2.1.1.1460.449
3ufuH4BNitric oxide synthase, brain1.14.13.390.449
3w0aDS5Vitamin D3 receptor/0.449
4enhFVXCholesterol 24-hydroxylase/0.449
4kfj1R0Dihydrofolate reductase1.5.1.30.449
4xymCOAAcyl-CoA synthetase (NDP forming)/0.449
1d3gBREDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.448
1jld0PPGag-Pol polyprotein/0.448
1sqbAZOCytochrome b/0.448
2nxeSAMRibosomal protein L11 methyltransferase2.1.10.448
2wpwACOOrf14/0.448
3ar4TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.448
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.448
3h3qH13Collagen type IV alpha-3-binding protein/0.448
3iqeH4MF420-dependent methylenetetrahydromethanopterin dehydrogenase1.5.98.10.448
3vt3VDXVitamin D3 receptor/0.448
4g210VPVitamin D3 receptor A/0.448
4ia7BIVVitamin D3 receptor A/0.448
4lxhC1EAlpha/beta hydrolase fold/0.448
4pnmNU1Tankyrase-22.4.2.300.448
5dbfNDPIridoid synthase1.3.1.990.448
1obnASVIsopenicillin N synthase1.21.3.10.447
1xp6AIUEstrogen receptor/0.447
2aclL05Oxysterols receptor LXR-alpha/0.447
2zevB71Geranylgeranyl pyrophosphate synthase/0.447
3cx5SMACytochrome b/0.447
3h6k33TCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
3l9lL9LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
3oiaA31Camphor 5-monooxygenase1.14.15.10.447
3qlzQLZUncharacterized protein/0.447
3wdsNADNADH-dependent quinuclidinone reductase/0.447
4boeCLRJapanin/0.447
4klrCHDFerrochelatase, mitochondrial4.99.1.10.447
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.447
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
4xsrUPGAlr3699 protein/0.447
1dkfBMSRetinoic acid receptor alpha/0.446
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
1olmVTQSEC14-like protein 2/0.446
1vj3TABDihydrofolate reductase1.5.1.30.446
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.446
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.446
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.446
2yiuSMACytochrome b/0.446
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
3pe6ZYHMonoglyceride lipase/0.446
3tqhNDPQuinone oxidoreductase/0.446
3w5tLHPVitamin D3 receptor/0.446
4bj9UHBTankyrase-22.4.2.300.446
4jaqCOAAlpha-pyrone synthesis polyketide synthase-like Pks112.3.10.446
4jx1CAMCamphor 5-monooxygenase1.14.15.10.446
4r20AERCytochrome P450 family 17 polypeptide 2/0.446
5ab7MLCNonspecific lipid-transfer protein, putative/0.446
3sn6P0GBeta-2 adrenergic receptor/0.446
1kk4ACOStreptogramin A acetyltransferase2.3.10.445
1rszDIHPurine nucleoside phosphorylase2.4.2.10.445
1s0zEB1Vitamin D3 receptor/0.445
1uzwCDHIsopenicillin N synthase1.21.3.10.445
1zeoC01Peroxisome proliferator-activated receptor gamma/0.445
2bxaC1FSerum albumin/0.445
2e9cB75Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.445
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.445
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.445
2pogWSTEstrogen receptor/0.445
2qjySMACytochrome b/0.445
2znq401Peroxisome proliferator-activated receptor delta/0.445
3f46I2C5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.445
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
3naxMP73-phosphoinositide-dependent protein kinase 12.7.11.10.445
4a862ANMajor pollen allergen Bet v 1-A/0.445
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
4g1z0VPVitamin D3 receptor A/0.445
4hyf1AKTankyrase-22.4.2.300.445
4ia2BIVVitamin D3 receptor A/0.445
4jbtASDCytochrome P450 monooxygenase/0.445
4nqgCZHMitrocomin/0.445
1ly3COGDihydrofolate reductase1.5.1.30.444
1ppjANYCytochrome b/0.444
2hcdBIVVitamin D3 receptor A/0.444
2q66ATPPoly(A) polymerase2.7.7.190.444
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3dxjNE6DNA-directed RNA polymerase subunit beta/0.444
3dxjNE6DNA-directed RNA polymerase subunit beta'/0.444
3r5zF42Uncharacterized protein/0.444
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.444
3vt65YIVitamin D3 receptor/0.444
4dtiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
4iae1DXAlr2278 protein/0.444
4iui1GQEstrogen receptor/0.444
4jvb1M0Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.444
4twpAXITyrosine-protein kinase ABL12.7.10.20.444
1bucFADAcyl-CoA dehydrogenase, short-chain specific1.3.8.10.443
1ie8KH1Vitamin D3 receptor/0.443
1p0hACOMycothiol acetyltransferase2.3.1.1890.443
2ewpTXFEstrogen-related receptor gamma/0.443
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.443
2o7pNAPRiboflavin biosynthesis protein RibD/0.443
2om9AJAPeroxisome proliferator-activated receptor gamma/0.443
3e5rNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.443
3gwfNAPCyclohexanone monooxygenase/0.443
3icrCOACoenzyme A disulfide reductase/0.443
3mjrAC2Deoxycytidine kinase2.7.1.740.443
3nksACJProtoporphyrinogen oxidase1.3.3.40.443
3p99LNPLanosterol 14-alpha-demethylase/0.443
3vt8YI3Vitamin D3 receptor/0.443
3zkyWT4Isopenicillin N synthase1.21.3.10.443
4a83DXCMajor pollen allergen Bet v 1-A/0.443
4bvaT3Ketimine reductase mu-crystallin1.5.1.250.443
4fhi0S4Vitamin D3 receptor A/0.443
4g3rCAMCamphor 5-monooxygenase1.14.15.10.443
5c3jUQ1Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.443
5c3jUQ1Succinate dehydrogenase cytochrome b560/0.443
5k2aZMAAdenosine receptor A2a/0.443
3qakUKAAdenosine receptor A2a/0.443
1disBDMDihydrofolate reductase1.5.1.30.442
1fmlRTLRetinol dehydratase/0.442
3ar6TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.442
3jynNDPQuinone oxidoreductase/0.442
3ue4DB8Tyrosine-protein kinase ABL12.7.10.20.442
3vrtYS2Vitamin D3 receptor/0.442
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.442
4bfpSWYTankyrase-22.4.2.300.442
4bfuZVUPantothenate kinase2.7.1.330.442
4fehFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.442
4j6dTESCytochrome P450 monooxygenase/0.442
4k4eK4ETankyrase-12.4.2.300.442
4o761M3Bromodomain-containing protein 4/0.442
1ia4TQ6Dihydrofolate reductase1.5.1.30.441
1lwlDSOCamphor 5-monooxygenase1.14.15.10.441
1p8dCO1Oxysterols receptor LXR-beta/0.441
2p1u4TNRetinoic acid receptor RXR-alpha/0.441
2rehFADNitroalkane oxidase1.7.3.10.441
2x9dITCTetracycline repressor protein class D/0.441
2za0MGILactoylglutathione lyase4.4.1.50.441
2znpK55Peroxisome proliferator-activated receptor delta/0.441
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
3ibdCPZCytochrome P450 2B61.14.130.441
3iqeF42F420-dependent methylenetetrahydromethanopterin dehydrogenase1.5.98.10.441
3oafOAGDihydrofolate reductase1.5.1.30.441
3opdHIEHeat shock protein 83/0.441
3up0D7SaceDAF-12/0.441
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.441
4bkqNAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.441
4e0u0MVCyclic dipeptide N-prenyltransferase/0.441
4o701QKBromodomain-containing protein 4/0.441
4xqcNADHomospermidine synthase2.5.1.440.441
4zasTYDCalS13/0.441
1ke9LS5Cyclin-dependent kinase 22.7.11.220.440
1p91SAM23S rRNA (guanine(745)-N(1))-methyltransferase/0.440
1tg56454-hydroxyphenylpyruvate dioxygenase1.13.11.270.440
1x2hLPALipoate-protein ligase A6.3.1.200.440
2acwUPGGlycosyltransferase/0.440
2ca0PXICytochrome P450 monooxygenase PikC/0.440
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
2j14GNIPeroxisome proliferator-activated receptor delta/0.440
3dfrMTXDihydrofolate reductase1.5.1.30.440
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.440
3gc9B45Mitogen-activated protein kinase 112.7.11.240.440
3gwfFADCyclohexanone monooxygenase/0.440
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3l0lHC3Nuclear receptor ROR-gamma/0.440
3n8xNIMProstaglandin G/H synthase 11.14.99.10.440
3oeyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
3p6nDSOCamphor 5-monooxygenase1.14.15.10.440
3saz043Malate synthase G/0.440
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.440
4azwATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.440
4bfvZVVPantothenate kinase2.7.1.330.440
4equG6ISerine/threonine-protein kinase 102.7.11.10.440
4iah1DXAlr2278 protein/0.440
4nc3ERM5-hydroxytryptamine receptor 2B/0.440
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.440
4xuhSFIPeroxisome proliferator-activated receptor gamma/0.440