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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
1ahnFMNFlavodoxin 1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1ahnFMNFlavodoxin 1/1.000
3esyFMNFlavodoxin/0.549
1j8qFMNFlavodoxin/0.547
1j9gFMNFlavodoxin/0.543
2mokFMNFlavodoxin 1/0.542
1cznFMNFlavodoxin/0.541
1ofvFMNFlavodoxin/0.529
1fx1FMNFlavodoxin/0.528
3f90FMNFlavodoxin/0.520
2v5uFMNFlavodoxin/0.516
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.507
3klbFMNUncharacterized protein/0.507
4fx2FMNFlavodoxin/0.501
4y7cFMNNADPH--cytochrome P450 reductase/0.501
5tgzFMNCannabinoid receptor 1/0.500
1q84TZ4Acetylcholinesterase3.1.1.70.498
1c7fFMNFlavodoxin/0.497
1akuFMNFlavodoxin/0.496
1azlFMNFlavodoxin/0.496
2bn4FMNNADPH--cytochrome P450 reductase/0.489
3eszFMNFlavodoxin/0.489
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.487
1wsbFMNFlavodoxin/0.486
2fcrFMNFlavodoxin/0.486
1akwFMNFlavodoxin/0.485
4oxxFMNCindoxin/0.485
4du6GTPGTP cyclohydrolase 1/0.484
1odcA8BAcetylcholinesterase3.1.1.70.483
3h3qH13Collagen type IV alpha-3-binding protein/0.482
3f6rFMNFlavodoxin/0.481
3kapFMNFlavodoxin/0.481
2pk3GDDGDP-6-deoxy-D-mannose reductase/0.480
2xupTZ5Acetylcholinesterase3.1.1.70.478
3ojxFMNNADPH--cytochrome P450 reductase/0.478
3c1kT15Prothrombin3.4.21.50.477
3qe2FMNNADPH--cytochrome P450 reductase/0.477
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
1akrFMNFlavodoxin/0.476
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.476
3qgi33FGenome polyprotein2.7.7.480.475
2z9dFMNFMN-dependent NADH-azoreductase/0.473
4araC56Acetylcholinesterase3.1.1.70.473
5xraFMNCannabinoid receptor 1/0.473
1njjORXOrnithine decarboxylase/0.472
2x93X93Angiotensin-converting enzyme3.4.15.10.472
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.471
3w5uFADFerredoxin/0.471
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.470
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.470
4mr72BVGamma-aminobutyric acid type B receptor subunit 1/0.469
2pb1NFGGlucan 1,3-beta-glucosidase/0.468
2b3dFADModulator of drug activity B/0.467
3kaqFMNFlavodoxin/0.467
3lzwNAPFerredoxin--NADP reductase 21.18.1.20.467
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.466
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.466
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
3qfrFMNNADPH--cytochrome P450 reductase/0.466
4briUNPEctonucleoside triphosphate diphosphohydrolase I/0.466
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.465
3rvhHQ2Lysine-specific demethylase 4A1.14.110.465
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.464
3wycNAPMeso-diaminopimelate D-dehydrogenase1.4.1.160.464
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.464
1bjkFADFerredoxin--NADP reductase1.18.1.20.463
1m4dCOAAminoglycoside 2'-N-acetyltransferase2.3.10.463
3go4SAHUncharacterized protein/0.463
1ycgFMNNitric oxide reductase10.462
4rrrA3TThreonine--tRNA ligase6.1.1.30.462
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.461
2xukTZ5Acetylcholinesterase3.1.1.70.461
5e5h0T1Succinyl-CoA:acetate CoA-transferase/0.461
1zgbA1EAcetylcholinesterase3.1.1.70.460
3fpkFADFerredoxin-NADP reductase/0.460
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.460
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.460
3zc3FADFerredoxin--NADP reductase1.18.1.20.459
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.459
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.459
2xdaJPS3-dehydroquinate dehydratase4.2.1.100.458
2xuhTZ4Acetylcholinesterase3.1.1.70.458
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.458
1cnfFADNitrate reductase [NADH]1.7.1.10.457
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.457
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.457
2fj1CTCTetracycline repressor protein class D/0.457
2wzySQXSoluble acetylcholine receptor/0.457
3s8pSAMHistone-lysine N-methyltransferase KMT5B2.1.1.430.457
2bb3SAHCobalamin biosynthesis precorrin-6Y methylase (CbiE)/0.456
2h8xFMNXenA/0.456
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3iu8T03Methionine aminopeptidase 2/0.456
4b4w9L9Bifunctional protein FolD/0.456
4c43FADFerredoxin--NADP reductase1.18.1.20.456
1xe65FPPlasmepsin-23.4.23.390.455
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.455
2a9y26AAdenosine kinase2.7.1.200.455
2gg9U16Methionine aminopeptidase/0.455
2wp9CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.455
2wp9CBESuccinate dehydrogenase cytochrome b556 subunit/0.455
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.455
4bqzGNPEctonucleoside triphosphate diphosphohydrolase 2/0.455
4e2dFMNDehydrogenase/0.455
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.455
4j8pFMNFlavodoxin/0.455
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.455
1e64FADFerredoxin--NADP reductase1.18.1.20.454
1gky5GPGuanylate kinase2.7.4.80.454
1xyvFMNFlavodoxin/0.454
2cekN8TAcetylcholinesterase3.1.1.70.454
3fp0FP015-O-acetyltransferase/0.454
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.454
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.454
1vfsDCSAlanine racemase/0.453
2futH1SHeparin and heparin-sulfate lyase/0.453
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
1r6uTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.452
1w35FADFerredoxin--NADP reductase1.18.1.20.452
2gyuHI6Acetylcholinesterase3.1.1.70.452
3wqmB29Diterpene synthase3.1.7.80.452
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
1amoFMNNADPH--cytochrome P450 reductase/0.451
1gaqFADFerredoxin/0.451
1gvrTNLPentaerythritol tetranitrate reductase/0.451
2ejzSAHDiphthine synthase/0.451
2g1n1IGRenin3.4.23.150.451
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.451
2wzmNA7Uncharacterized oxidoreductase MSMEG_2407/MSMEI_2346/0.451
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
4af6FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.451
4af7FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.451
4b1jA1RPoly(ADP-ribose) glycohydrolase3.2.1.1430.451
1dgmADNAdenosine kinase2.7.1.200.450
1lkeDOGBilin-binding protein/0.450
1w6rGNTAcetylcholinesterase3.1.1.70.450
1yobFMNFlavodoxin 2/0.450
2j5bTYETyrosine--tRNA ligase6.1.1.10.450
2whqHI6Acetylcholinesterase3.1.1.70.450
3mhpFADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.450
4k9oTPPBenzoylformate decarboxylase4.1.1.70.450
1ex75GPGuanylate kinase2.7.4.80.449
2fx2FMNFlavodoxin/0.449
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3gonANPPhosphomevalonate kinase/0.449
3gxfIFMGlucosylceramidase3.2.1.450.449
3r9g7MCMccE protein/0.449
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.449
4b1hAR6Poly(ADP-ribose) glycohydrolase3.2.1.1430.449
4n1gCEIObelin/0.449
4r81FMNPredicted NADH dehydrogenase/0.449
5dw50T1Succinyl-CoA:acetate CoA-transferase/0.449
1bxqPP8Penicillopepsin-13.4.23.200.448
1dx6GNTAcetylcholinesterase3.1.1.70.448
1pq944BOxysterols receptor LXR-beta/0.448
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.448
2vq7NAPPutative flavin-containing monooxygenase/0.448
2xufTZ4Acetylcholinesterase3.1.1.70.448
2xugTZ4Acetylcholinesterase3.1.1.70.448
3pchCHBProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.448
4bftZVTPantothenate kinase2.7.1.330.448
4i1c1BEBeta-secretase 13.4.23.460.448
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.448
4to0DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.448
5dp2NAPCurF/0.448
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.447
1x1cSAHC-20 methyltransferase/0.447
2ckmAA7Acetylcholinesterase3.1.1.70.447
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
2p99YE6Methionine aminopeptidase/0.447
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.447
3otwCOAPhosphopantetheine adenylyltransferase/0.447
4lm4JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
4u140HKMuscarinic acetylcholine receptor M3/0.447
1qpl587Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.446
1ycfFMNNitric oxide reductase10.446
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.446
2ed3SAHDiphthine synthase/0.446
2o6hINI6,7-dimethyl-8-ribityllumazine synthase 12.5.1.780.446
3djjFADGlutathione reductase, mitochondrial1.8.1.70.446
3hf3FMNChromate reductase/0.446
3q9bB3NAcetylpolyamine amidohydrolase/0.446
3v2uATPProtein GAL3/0.446
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.446
4j7hTRHPCZA361.3/0.446
5xr8FMNCannabinoid receptor 1/0.446
1a9cGTPGTP cyclohydrolase 13.5.4.160.445
1h6cNDPGlucose--fructose oxidoreductase1.1.99.280.445
2gesCOKPantothenate kinase2.7.1.330.445
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.445
2zseACPPantothenate kinase2.7.1.330.445
3kp0Z98D-ornithine 4,5-aminomutase subunit beta/0.445
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.445
4b7zQ4QAcetylcholinesterase3.1.1.70.445
4y17LAETranscriptional regulator of ftsQAZ gene cluster/0.445
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.444
1rz1NADPhenol 2-hydroxylase component B/0.444
1toiHCIAspartate aminotransferase2.6.1.10.444
2qzlIXSBeta-secretase 13.4.23.460.444
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.444
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.444
3hbfMYCFlavonoid 3-O-glucosyltransferase2.4.10.444
3rsv3RSBeta-secretase 13.4.23.460.444
3swcSAHHistone-lysine N-methyltransferase EHMT1/0.444
4fl0PLPAminotransferase ALD1, chloroplastic2.6.10.444
4g95OAGDihydrofolate reductase1.5.1.30.444
1j9zFADNADPH--cytochrome P450 reductase/0.443
2ea4F79Methionine aminopeptidase 2/0.443
2f99AKVAklanonic acid methyl ester cyclase AcmA5.5.1.230.443
2j3qTFLAcetylcholinesterase3.1.1.70.443
2q92B23Methionine aminopeptidase/0.443
2ywlFADThioredoxin reductase related protein/0.443
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.443
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.443
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.443
3u8l09QAcetylcholine-binding protein/0.443
4f9gC2EStimulator of interferon genes protein/0.443
4lcnGNGCytidine and deoxycytidylate deaminase zinc-binding region/0.443
4psbGA3Cytokinin-specific binding protein/0.443
4s1hADPPyridoxal kinase, putative/0.443
1b2lNDCAlcohol dehydrogenase1.1.1.10.442
1p0pBCHCholinesterase3.1.1.80.442
1qtiGNTAcetylcholinesterase3.1.1.70.442
1r6tTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.442
1votHUPAcetylcholinesterase3.1.1.70.442
1w19T5P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
1xp8AGSProtein RecA/0.442
3c8bARG_ARG_GLY_ILE_NH2Botulinum neurotoxin type A3.4.24.690.442
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.442
3djgFADGlutathione reductase, mitochondrial1.8.1.70.442
3h3r14HCollagen type IV alpha-3-binding protein/0.442
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.442
4m0cFMNFMN-dependent NADH-azoreductase 1/0.442
5eghPCEctonucleotide pyrophosphatase/phosphodiesterase family member 6/0.442
1bx1FADFerredoxin--NADP reductase, chloroplastic1.18.1.20.441
1ppl1Z7Penicillopepsin-13.4.23.200.441
1yw8A75Methionine aminopeptidase 2/0.441
2ea2F77Methionine aminopeptidase 2/0.441
2gg2U12Methionine aminopeptidase/0.441
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3sxjSAMPutative methyltransferase/0.441
3tqxPLP2-amino-3-ketobutyrate coenzyme A ligase/0.441
3v0o4GWHisto-blood group ABO system transferase/0.441
4bmpFMNProtein NrdI/0.441
1rkwPNTHTH-type transcriptional regulator QacR/0.440
1tkaN3TTransketolase 12.2.1.10.440
1zgcA2EAcetylcholinesterase3.1.1.70.440
2geuCOKPantothenate kinase2.7.1.330.440
2rc6FADFerredoxin--NADP reductase/0.440
2rqfJH3Hemolymph juvenile hormone binding protein/0.440
2xncFADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.440
3pce3HPProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.440
3pce3HPProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.440
4da7AC2Purine nucleoside phosphorylase DeoD-type2.4.2.10.440
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4qfyDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.440
5a27MYAGlycylpeptide N-tetradecanoyltransferase/0.440