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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
3aosJH2Hemolymph juvenile hormone binding protein

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3aosJH2Hemolymph juvenile hormone binding protein/1.000
4bfxZVXPantothenate kinase2.7.1.330.495
3c3xNAPEugenol synthase 11.1.1.3180.494
2rqfJH3Hemolymph juvenile hormone binding protein/0.491
1upw444Oxysterols receptor LXR-beta/0.489
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.489
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.487
2vcmM11Isopenicillin N synthase1.21.3.10.475
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.473
3h3t16HCollagen type IV alpha-3-binding protein/0.469
1p91SAM23S rRNA (guanine(745)-N(1))-methyltransferase/0.468
3h3r14HCollagen type IV alpha-3-binding protein/0.468
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.467
3zkyWT4Isopenicillin N synthase1.21.3.10.467
2xuoTZ4Acetylcholinesterase3.1.1.70.466
3cx4ADPGlycogen synthase2.4.1.210.466
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.465
2qw8NAPEugenol synthase 11.1.1.3180.465
3ekuCY9Actin-5C/0.464
4a81DXCMajor pollen allergen Bet v 1-A/0.463
1qoqIGPTryptophan synthase alpha chain/0.462
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
4e2yJHZMethyltransferase/0.461
4jlj1NMDeoxycytidine kinase2.7.1.740.461
4pnmNU1Tankyrase-22.4.2.300.461
1dtpAPUDiphtheria toxin/0.460
2y6fM9FIsopenicillin N synthase1.21.3.10.460
2k62ITLFatty acid-binding protein, liver/0.458
4bftZVTPantothenate kinase2.7.1.330.458
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.457
1r2jFADFkbI/0.457
1p0pBCHCholinesterase3.1.1.80.456
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.456
2fzjDH3Dihydrofolate reductase1.5.1.30.456
3wavDWVEctonucleotide pyrophosphatase/phosphodiesterase family member 23.1.4.390.456
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.456
1b2lNDCAlcohol dehydrogenase1.1.1.10.453
1blzACVIsopenicillin N synthase1.21.3.10.453
3fktSIIBeta-secretase 13.4.23.460.453
3fp0FP015-O-acetyltransferase/0.453
1u65CP0Acetylcholinesterase3.1.1.70.452
2imfTOM2-hydroxychromene-2-carboxylate isomerase5.99.1.40.452
2qimZEAClass 10 plant pathogenesis-related protein/0.452
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.451
2vprTDCTetracycline repressor protein class H/0.451
3zoiM2WIsopenicillin N synthase1.21.3.10.451
4jlk1NODeoxycytidine kinase2.7.1.740.451
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.450
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.450
4bfsZVSPantothenate kinase2.7.1.330.450
1j49NADD-lactate dehydrogenase1.1.1.280.449
1x8lOXRRetinol dehydratase/0.449
4a8v2ANMajor pollen allergen Bet v 1-J/0.449
4f0e0RUPoly [ADP-ribose] polymerase 152.4.2.300.449
1fmlRTLRetinol dehydratase/0.448
2xaaNADSecondary alcohol dehydrogenase/0.448
1bk0ACVIsopenicillin N synthase1.21.3.10.447
1r5hAO2Methionine aminopeptidase 2/0.447
2vbpVB1Isopenicillin N synthase1.21.3.10.447
2xvv9DNSerum albumin/0.447
2xvw9NRSerum albumin/0.447
3zc3FADFerredoxin--NADP reductase1.18.1.20.447
1pd9CO4Dihydrofolate reductase1.5.1.30.446
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.446
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3nmpPYVAbscisic acid receptor PYL2/0.446
4g95OAGDihydrofolate reductase1.5.1.30.446
1q83TZ5Acetylcholinesterase3.1.1.70.445
1r5gAO1Methionine aminopeptidase 2/0.445
1xnjADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 12.7.1.250.445
3c1oNAPEugenol synthase/0.445
3vt7VDXVitamin D3 receptor/0.445
4eqrCOACoenzyme A disulfide reductase/0.445
5hynSAHHistone-lysine N-methyltransferase EZH22.1.1.430.445
1w4lGL8Acetylcholinesterase3.1.1.70.444
1zgbA1EAcetylcholinesterase3.1.1.70.444
2ekpNAD2-deoxy-D-gluconate 3-dehydrogenase/0.444
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.444
3fr5I4AFatty acid-binding protein, adipocyte/0.444
4a84DXCMajor pollen allergen Bet v 1-A/0.444
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.444
4c72TLG3-oxoacyl-ACP synthase/0.444
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.444
4hy6FJ1Heat shock protein HSP 90-alpha/0.444
4jqh1MFAlr2278 protein/0.444
4o7uTHFThymidylate synthase/0.444
1p8dCO1Oxysterols receptor LXR-beta/0.443
2uxuNARHTH-type transcriptional regulator TtgR/0.443
3dcsMZMCarbonic anhydrase 24.2.1.10.443
3fhxPLPPyridoxal kinase2.7.1.350.443
3ho9N3A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.443
4ijrNDPD-arabinose dehydrogenase [NAD(P)+] heavy chain1.1.1.1170.443
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.443
1hfqMOTDihydrofolate reductase1.5.1.30.442
1obnASVIsopenicillin N synthase1.21.3.10.442
1s3uTQDDihydrofolate reductase1.5.1.30.442
2iyaZIOOleandomycin glycosyltransferase/0.442
3h3sH15Collagen type IV alpha-3-binding protein/0.442
3zkuHCVIsopenicillin N synthase1.21.3.10.442
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
1pq6965Oxysterols receptor LXR-beta/0.441
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.441
1rkwPNTHTH-type transcriptional regulator QacR/0.441
2gjlFMNNitronate monooxygenase1.13.12.160.441
2gv8NDPThiol-specific monooxygenase1.14.130.441
2xviFADPutative flavin-containing monooxygenase/0.441
3ar5TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.441
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.441
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.441
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.441
4l1xNAPAldo-keto reductase family 1 member C2/0.441
4m87NADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.441
1vrqFONSubunit alpha of sarocosine oxidase/0.440
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2vqbNAPPutative flavin-containing monooxygenase/0.440
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440