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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
3klbFMNUncharacterized protein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3klbFMNUncharacterized protein/1.000
4j8pFMNFlavodoxin/0.541
4gi5FADPutative NAD(P)H dehydrogenase (Quinone)/0.509
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.496
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.496
1amoFMNNADPH--cytochrome P450 reductase/0.487
4qofFMNRibosyldihydronicotinamide dehydrogenase [quinone]/0.485
4r81FMNPredicted NADH dehydrogenase/0.483
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.480
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.480
3g5mFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.480
3d91REMRenin3.4.23.150.478
4bfxZVXPantothenate kinase2.7.1.330.476
4qoeFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.473
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.469
4bftZVTPantothenate kinase2.7.1.330.469
2xveFADPutative flavin-containing monooxygenase/0.465
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.464
3zhoFMNNAD(P)H dehydrogenase (quinone)/0.464
3q7fED2Uncharacterized protein/0.463
3vkjFNRIsopentenyl-diphosphate delta-isomerase/0.463
1cf3FADGlucose oxidase1.1.3.40.462
2qmyFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.462
1ry8RUTAldo-keto reductase family 1 member C3/0.461
3ojwFMNNADPH--cytochrome P450 reductase/0.461
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.461
5dp2NAPCurF/0.461
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.459
1z6tADPApoptotic protease-activating factor 1/0.457
2xuqTZ4Acetylcholinesterase3.1.1.70.457
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.456
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.456
1ry0PG2Aldo-keto reductase family 1 member C3/0.455
2ifaFMNUncharacterized protein/0.455
2zryFNRIsopentenyl-diphosphate delta-isomerase/0.454
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.454
4j7hTRHPCZA361.3/0.454
4zvlFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.454
3hl0NADMaleylacetate reductase/0.453
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.453
1n95FTHProtein farnesyltransferase subunit beta2.5.1.580.452
4b78KGGBeta-secretase 13.4.23.460.452
4nv10FXFormyl transferase/0.452
4zvnFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.452
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.452
2zrvFNRIsopentenyl-diphosphate delta-isomerase/0.451
3wagTYDGlycosyltransferase/0.451
4drhRAPSerine/threonine-protein kinase mTOR2.7.11.10.451
4drhRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.451
4wx2F6FTryptophan synthase alpha chain/0.451
4wx2F6FTryptophan synthase beta chain4.2.1.200.451
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.450
3e33ED7Protein farnesyltransferase subunit beta2.5.1.580.450
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.450
4acuQN7Beta-secretase 13.4.23.460.450
1q84TZ4Acetylcholinesterase3.1.1.70.449
1qtiGNTAcetylcholinesterase3.1.1.70.449
2ikuLIYRenin3.4.23.150.449
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.449
4n9qFMNFMN-dependent NADH-azoreductase 1/0.449
1fmlRTLRetinol dehydratase/0.448
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.448
2hpvFMNFMN-dependent NADH-azoreductase1.70.448
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.447
2iko7IGRenin3.4.23.150.447
4bfyZVYPantothenate kinase2.7.1.330.447
1qr2FADRibosyldihydronicotinamide dehydrogenase [quinone]/0.446
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.446
4j7gTRHPCZA361.3/0.446
4q0kGA3Phytohormone-binding protein/0.446
3cluFADElectron transfer flavoprotein subunit alpha/0.445
3f90FMNFlavodoxin/0.445
3pz23PZGeranylgeranyl transferase type-2 subunit beta2.5.1.600.445
3vilSA0Beta-glucosidase/0.445
1ozpACOMycothiol acetyltransferase2.3.1.1890.444
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
2g8yNADHydroxycarboxylate dehydrogenase B/0.444
2geuCOKPantothenate kinase2.7.1.330.444
2xlrFADPutative flavin-containing monooxygenase/0.444
3irhDTPHD domain protein/0.444
4rvfTYDD-mycarose 3-C-methyltransferase/0.444
2gv8NDPThiol-specific monooxygenase1.14.130.443
2xlpNAPPutative flavin-containing monooxygenase/0.443
2il2LIXRenin3.4.23.150.442
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.442
4b65NDPL-ornithine N(5)-monooxygenase/0.442
5irnADPNucleotide binding oligomerization domain containing 2/0.442
1s63778Protein farnesyltransferase subunit beta2.5.1.580.441
1yplRA8Prothrombin3.4.21.50.441
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.441
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.441
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.441
2ohiFMNType A flavoprotein FprA10.441
3cow52HPantothenate synthetase6.3.2.10.441
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.441
4f7iNAD3-isopropylmalate dehydrogenase1.1.1.850.441
1esmCOAPantothenate kinase2.7.1.330.440
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1nsgRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.440
1nsgRADSerine/threonine-protein kinase mTOR2.7.11.10.440
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.440
1ta6177Prothrombin3.4.21.50.440
2g1s4IGRenin3.4.23.150.440
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.440
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.440
4h1e10JBeta-secretase 13.4.23.460.440
4n65FMNFMN-dependent NADH-azoreductase 1/0.440
5fm7ADPRuvB-like helicase/0.440