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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
3klbFMNUncharacterized protein

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3klbFMNUncharacterized protein/1.000
4j8pFMNFlavodoxin/0.541
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.494
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.494
2ejzSAHDiphthine synthase/0.478
4qofFMNRibosyldihydronicotinamide dehydrogenase [quinone]/0.476
4bftZVTPantothenate kinase2.7.1.330.475
3g5mFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.472
3q7fED2Uncharacterized protein/0.471
3d91REMRenin3.4.23.150.470
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.469
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.469
4bfxZVXPantothenate kinase2.7.1.330.469
4r81FMNPredicted NADH dehydrogenase/0.469
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.467
4qoeFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.466
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.464
3zhoFMNNAD(P)H dehydrogenase (quinone)/0.464
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.464
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.463
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.462
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.462
1n95FTHProtein farnesyltransferase subunit beta2.5.1.580.459
2qmyFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.458
2xviFADPutative flavin-containing monooxygenase/0.458
1e66HUXAcetylcholinesterase3.1.1.70.456
1z6tADPApoptotic protease-activating factor 1/0.456
2gjlFMNNitronate monooxygenase1.13.12.160.455
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.455
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.455
5dp2NAPCurF/0.455
2xuqTZ4Acetylcholinesterase3.1.1.70.454
3m30COMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.454
3m30COMMethyl-coenzyme M reductase I subunit beta2.8.4.10.454
4j7hTRHPCZA361.3/0.454
1ry8RUTAldo-keto reductase family 1 member C3/0.453
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.453
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.453
2zryFNRIsopentenyl-diphosphate delta-isomerase/0.452
4ead0NPThymidine phosphorylase2.4.2.40.452
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.452
2zrvFNRIsopentenyl-diphosphate delta-isomerase/0.451
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.450
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.450
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.450
2ylrNAPPhenylacetone monooxygenase1.14.13.920.450
3b05IPEIsopentenyl-diphosphate delta-isomerase/0.450
3hl0NADMaleylacetate reductase/0.450
1cf3FADGlucose oxidase1.1.3.40.449
1q84TZ4Acetylcholinesterase3.1.1.70.449
4mr92BXGamma-aminobutyric acid type B receptor subunit 1/0.449
4zvlFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.449
1ry0PG2Aldo-keto reductase family 1 member C3/0.448
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.448
3cluFADElectron transfer flavoprotein subunit alpha/0.448
4acuQN7Beta-secretase 13.4.23.460.448
1ni1HFPProtein farnesyltransferase subunit beta2.5.1.580.447
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.447
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.447
3vkjFNRIsopentenyl-diphosphate delta-isomerase/0.447
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.447
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.446
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.446
4b78KGGBeta-secretase 13.4.23.460.446
4bfyZVYPantothenate kinase2.7.1.330.446
4hcy0YNTransketolase/0.446
4n9qFMNFMN-dependent NADH-azoreductase 1/0.446
4q0kGA3Phytohormone-binding protein/0.446
2whqHI6Acetylcholinesterase3.1.1.70.445
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.445
3e33ED7Protein farnesyltransferase subunit beta2.5.1.580.445
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.445
3v2uATPProtein GAL3/0.445
4b7754MBeta-secretase 13.4.23.460.445
4relKMPGlycosyltransferase/0.445
4zvnFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.445
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.444
1qtiGNTAcetylcholinesterase3.1.1.70.444
1tllFMNNitric oxide synthase, brain1.14.13.390.444
2geuCOKPantothenate kinase2.7.1.330.444
2pncCLUPrimary amine oxidase, liver isozyme/0.444
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.444
4j7gTRHPCZA361.3/0.444
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.444
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
2iejS48Protein farnesyltransferase subunit beta2.5.1.580.443
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.443
3vilSA0Beta-glucosidase/0.443
4i1c1BEBeta-secretase 13.4.23.460.443
4nv10FXFormyl transferase/0.443
1qr2FADRibosyldihydronicotinamide dehydrogenase [quinone]/0.442
2zsaADPPantothenate kinase2.7.1.330.442
3to3ATPPetrobactin biosynthesis protein AsbB/0.442
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.441
2yoj8Y6Genome polyprotein2.7.7.480.441
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4ey6GNTAcetylcholinesterase3.1.1.70.441
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.441
2xlrFADPutative flavin-containing monooxygenase/0.440
3h3r14HCollagen type IV alpha-3-binding protein/0.440
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.440
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440