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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
1qgzFADFerredoxin--NADP reductase1.18.1.2

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1qgzFADFerredoxin--NADP reductase1.18.1.21.000
1e63FADFerredoxin--NADP reductase1.18.1.20.883
1qgyFADFerredoxin--NADP reductase1.18.1.20.710
1h85FADFerredoxin--NADP reductase1.18.1.20.700
1bjkFADFerredoxin--NADP reductase1.18.1.20.664
1e62FADFerredoxin--NADP reductase1.18.1.20.664
1ogiFADFerredoxin--NADP reductase1.18.1.20.655
1h42FADFerredoxin--NADP reductase1.18.1.20.651
1e64FADFerredoxin--NADP reductase1.18.1.20.650
2b5oFADFerredoxin--NADP reductase1.18.1.20.650
1qh0FADFerredoxin--NADP reductase1.18.1.20.648
4c43FADFerredoxin--NADP reductase1.18.1.20.643
4bprFADFerredoxin--NADP reductase1.18.1.20.642
1ogjFADFerredoxin--NADP reductase1.18.1.20.641
1gjrFADFerredoxin--NADP reductase1.18.1.20.639
1queFADFerredoxin--NADP reductase1.18.1.20.638
1fndFADFerredoxin--NADP reductase, chloroplastic1.18.1.20.637
1gr1FADFerredoxin--NADP reductase1.18.1.20.634
1fncFDAFerredoxin--NADP reductase, chloroplastic1.18.1.20.633
3zbtFADFerredoxin--NADP reductase1.18.1.20.617
1b2rFADFerredoxin--NADP reductase1.18.1.20.615
3vo2FADFerredoxin--NADP reductase/0.610
1bx1FADFerredoxin--NADP reductase, chloroplastic1.18.1.20.608
4af7FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.607
3zc3FADFerredoxin--NADP reductase1.18.1.20.605
1gawFADFerredoxin/0.604
1fnbFADFerredoxin--NADP reductase, chloroplastic1.18.1.20.592
1sm4FADFerredoxin--NADP reductase/0.591
1go2FADFerredoxin--NADP reductase1.18.1.20.587
3mhpFADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.587
1bx0FADFerredoxin--NADP reductase, chloroplastic1.18.1.20.584
1ewyFADFerredoxin--NADP reductase1.18.1.20.583
2rc6FADFerredoxin--NADP reductase/0.580
4af6FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.579
3w5uFADFerredoxin/0.573
1w87FADFerredoxin--NADP reductase1.18.1.20.571
1w35FADFerredoxin--NADP reductase1.18.1.20.569
1gaqFADFerredoxin/0.564
3fpkFADFerredoxin-NADP reductase/0.552
2rc5FADFerredoxin--NADP reductase/0.542
1j9zFADNADPH--cytochrome P450 reductase/0.538
2xncFADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.532
3qftFADNADPH--cytochrome P450 reductase/0.529
3jqrFADFerredoxin--NADP reductase, apicoplast/0.521
3qfsFADNADPH--cytochrome P450 reductase/0.521
4yaoFADNADPH--cytochrome P450 reductase/0.515
1amoFADNADPH--cytochrome P450 reductase/0.509
4uajFADNa(+)-translocating NADH-quinone reductase subunit F/0.508
1lnmDTXBilin-binding protein/0.506
4i101BSBeta-secretase 13.4.23.460.498
2ok8FADFerredoxin--NADP reductase, apicoplast/0.495
4j7hTRHPCZA361.3/0.495
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.495
2piaFMNPhthalate dioxygenase reductase/0.493
1ja1FADNADPH--cytochrome P450 reductase/0.492
5a4vQUEGlutathione S-transferase F22.5.1.180.490
3rtnRTNBeta-secretase 13.4.23.460.487
1thnADPAnti-sigma F factor/0.484
1f20FADNitric oxide synthase, brain1.14.13.390.483
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.482
3fr5I4AFatty acid-binding protein, adipocyte/0.482
5ah5LSSLeucine--tRNA ligase/0.481
3er93ATPoly(A) polymerase catalytic subunit2.7.7.190.479
3wqmB29Diterpene synthase3.1.7.80.479
4gm4TZDBenzoylformate decarboxylase4.1.1.70.479
1a8pFADFerredoxin--NADP reductase/0.478
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.478
3rsv3RSBeta-secretase 13.4.23.460.478
3mjrAC2Deoxycytidine kinase2.7.1.740.476
3otwCOAPhosphopantetheine adenylyltransferase/0.476
4gg1TZDBenzoylformate decarboxylase4.1.1.70.476
5dn1AMZPhosphoribosyl isomerase A5.3.1.160.473
3fhxPLPPyridoxal kinase2.7.1.350.472
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.472
3t4hMD5Alpha-ketoglutarate-dependent dioxygenase AlkB1.14.11.330.472
1yciNDFHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.471
2nnqT4BFatty acid-binding protein, adipocyte/0.471
2vt4P32Beta-1 adrenergic receptor/0.471
1cqxFADFlavohemoprotein/0.470
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.470
2vnjFADNADPH:ferredoxin reductase/0.470
2x06NADL-sulfolactate dehydrogenase/0.470
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.469
2w6zL21Biotin carboxylase6.3.4.140.469
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.469
1gky5GPGuanylate kinase2.7.4.80.468
4bjcRPBTankyrase-22.4.2.300.468
4f3gKAIGlutamate receptor 3/0.468
1a9cGTPGTP cyclohydrolase 13.5.4.160.467
1g63FMNEpidermin decarboxylase4.1.10.467
2ejzSAHDiphthine synthase/0.467
2rqfJH3Hemolymph juvenile hormone binding protein/0.467
1pq944BOxysterols receptor LXR-beta/0.466
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.466
4zu44TGWxcM-like protein/0.466
2dsgSAHDiphthine synthase/0.465
3rbaCODPhosphopantetheine adenylyltransferase/0.464
3vkjFNRIsopentenyl-diphosphate delta-isomerase/0.464
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.464
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.464
5bu2ADPUncharacterized protein/0.464
1touB1VFatty acid-binding protein, adipocyte/0.463
3fr28CAFatty acid-binding protein, adipocyte/0.463
3ce0P34Poly [ADP-ribose] polymerase 32.4.2.300.462
3qgf46FGenome polyprotein2.7.7.480.462
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.462
1pqc444Oxysterols receptor LXR-beta/0.461
3phjDHKShikimate dehydrogenase (NADP(+))/0.461
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.460
2vd0D27Hematopoietic prostaglandin D synthase/0.460
2zrvFNRIsopentenyl-diphosphate delta-isomerase/0.460
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.459
2ptfFMNUncharacterized protein MTH_863/0.459
3cb2GDPTubulin gamma-1 chain/0.459
3rgaILDEpoxide hydrolase LasB5.5.10.459
4ckrDI1Epithelial discoidin domain-containing receptor 12.7.10.10.459
1e79ATPATP synthase subunit alpha, mitochondrial/0.458
1e79ATPATP synthase subunit beta, mitochondrial3.6.3.140.458
2dv3SAHDiphthine synthase/0.458
2iu8UD1UDP-3-O-acylglucosamine N-acyltransferase2.3.10.458
3fr4F8AFatty acid-binding protein, adipocyte/0.458
3ivcFG4Pantothenate synthetase6.3.2.10.458
4bjbP34Tankyrase-22.4.2.300.458
4fhd0TTSpore photoproduct lyase/0.458
4fpy0V8Sialidase B3.2.1.180.458
4j7gTRHPCZA361.3/0.458
1kyvRBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.457
1n3sGTPGTP cyclohydrolase 13.5.4.160.457
2jf6S55Strictosidine-O-beta-D-glucosidase3.2.1.1050.457
2uuoLK3UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.457
2zs9ADPPantothenate kinase2.7.1.330.457
3nh8DC2N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming)3.5.1.1140.457
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.457
3vf60H6Glucokinase2.7.1.20.457
4j0v1H7Beta-secretase 13.4.23.460.457
4jyzATPGlutamine--tRNA ligase6.1.1.180.457
2a2cADPN-acetylgalactosamine kinase2.7.1.1570.456
3i0pNADMalate dehydrogenase, putative/0.456
3p2oNADBifunctional protein FolD/0.456
4n4wSNTSmoothened homolog/0.456
1qoqIGPTryptophan synthase alpha chain/0.455
1rkwPNTHTH-type transcriptional regulator QacR/0.455
1yw8A75Methionine aminopeptidase 2/0.455
2gevCOKPantothenate kinase2.7.1.330.455
2pswCOAN-alpha-acetyltransferase 50/0.455
3n3aFMNProtein NrdI/0.455
3ske054Genome polyprotein2.7.7.480.455
1fdrFADFerredoxin--NADP reductase1.18.1.20.454
3c0zSHHHistone deacetylase 73.5.1.980.454
3ed1GA3Gibberellin receptor GID1/0.454
3pftFMNFlavin reductase/0.454
4bfxZVXPantothenate kinase2.7.1.330.454
4rrrA3TThreonine--tRNA ligase6.1.1.30.454
1lkeDOGBilin-binding protein/0.453
1sdwIYTPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.453
2gjnFMNNitronate monooxygenase1.13.12.160.453
2pb6SAHDiphthine synthase/0.453
3iexGMPPurine nucleoside phosphorylase/0.453
4b4vL34Bifunctional protein FolD/0.453
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.453
1z41FMNNADPH dehydrogenase/0.452
2a9y26AAdenosine kinase2.7.1.200.452
2an9GDPGuanylate kinase2.7.4.80.452
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.452
2vn1FK5Peptidylprolyl isomerase/0.452
2y882ERPhosphoribosyl isomerase A5.3.1.160.452
3ekuCY9Actin-5C/0.452
3fazNOSPurine nucleoside phosphorylase/0.452
3fsjD7KBenzoylformate decarboxylase4.1.1.70.452
3hl0NADMaleylacetate reductase/0.452
3tr05GPGuanylate kinase/0.452
3wagTYDGlycosyltransferase/0.452
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.452
5dp2NAPCurF/0.452
1x1cSAHC-20 methyltransferase/0.451
2cdaNAPGlucose 1-dehydrogenase/0.451
3uph0C1Genome polyprotein2.7.7.480.451
3zj7C1KStrictosidine-O-beta-D-glucosidase3.2.1.1050.451
4jq2SUZAldo-keto reductase family 1 member C2/0.451
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.451
1u2rSO1Elongation factor 2/0.450
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.450
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.450
3af1GDPPantothenate kinase2.7.1.330.450
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.450
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.450
3klbFMNUncharacterized protein/0.450
3nt2NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.450
3nt5NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.450
3q9bB3NAcetylpolyamine amidohydrolase/0.450
1icpFMN12-oxophytodienoate reductase 11.3.1.420.449
1o2g696Prothrombin3.4.21.50.449
1r58AO5Methionine aminopeptidase 2/0.449
2gz7D3FOrf1a polyprotein/0.449
2jl1NAPTriphenylmethane reductase/0.449
2vqjTFGHistone deacetylase 43.5.1.980.449
2vz0D64Pteridine reductase/0.449
3dd0EZLCarbonic anhydrase 24.2.1.10.449
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.449
3wquATPCell division protein FtsA/0.449
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.449
1cl2PPGCystathionine beta-lyase MetC4.4.1.80.448
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.448
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.448
1s7gNADNAD-dependent protein deacylase 2/0.448
2pb4SAHDiphthine synthase/0.448
2re8GSUGlutamine--tRNA ligase6.1.1.180.448
3bi6396Wee1-like protein kinase2.7.10.20.448
3dr7GPDGDP-perosamine synthase/0.448
3vt7VDXVitamin D3 receptor/0.448
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.447
1lkdBP6Biphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.447
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.447
2bgiFADNADPH:ferredoxin reductase/0.447
2e8qSAHDiphthine synthase/0.447
2watCOAFatty acid synthase subunit alpha2.3.1.860.447
3fhxPXLPyridoxal kinase2.7.1.350.447
3q43D66M1 family aminopeptidase3.4.110.447
4usqFADPyridine nucleotide-disulfide oxidoreductase/0.447
1cnfFADNitrate reductase [NADH]1.7.1.10.446
1ejeFMNProtein MTH_152/0.446
1t4cCOAFormyl-CoA:oxalate CoA-transferase/0.446
1trkTPPTransketolase 12.2.1.10.446
2ed3SAHDiphthine synthase/0.446
2eeqSAHDiphthine synthase/0.446
3dhaC6LN-acyl homoserine lactonase AiiA3.1.1.810.446
3n87N873-dehydroquinate dehydratase4.2.1.100.446
4bfuZVUPantothenate kinase2.7.1.330.446
4h0vNADIota toxin component Ia/0.446
4j0y1H6Beta-secretase 13.4.23.460.446
4nhyPD2Prolyl 3-hydroxylase OGFOD11.14.110.446
1bcuPRLProthrombin3.4.21.50.445
2fsvNAPNAD(P) transhydrogenase subunit beta1.6.1.20.445
2gpjFADSiderophore-interacting protein/0.445
2r5nTPPTransketolase 1/0.445
3e4aQIXInsulin-degrading enzyme3.4.24.560.445
3ihzFK5Peptidylprolyl isomerase/0.445
3p0fBAUUridine phosphorylase 22.4.2.30.445
3sqxANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.445
4b65FADL-ornithine N(5)-monooxygenase/0.445
4b7754MBeta-secretase 13.4.23.460.445
4bfwZVWPantothenate kinase2.7.1.330.445
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.445
1f8gNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.444
1kyyINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.444
1opmIYGPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.444
1qrtATPGlutamine--tRNA ligase6.1.1.180.444
1w19T4P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.444
2pk3GDDGDP-6-deoxy-D-mannose reductase/0.444
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.444
2qo6CHDFatty acid-binding protein 10-A, liver basic/0.444
2wjoQUDBeta-secretase 13.4.23.460.444
3l9mL9McAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
3qwc98PProthrombin3.4.21.50.444
4bfvZVVPantothenate kinase2.7.1.330.444
4dya0MFNucleoprotein/0.444
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
4eepFMNPhototropin-22.7.11.10.444
4h3i10VBeta-secretase 13.4.23.460.444
4l7vSAHProtein-L-isoaspartate O-methyltransferase/0.444
4rtbSAMPutative thiazole biosynthesis protein ThiH/0.444
1gt5BZQOdorant-binding protein/0.443
1hzzNAPNAD(P) transhydrogenase subunit beta1.6.1.20.443
1jyw147Beta-galactosidase3.2.1.230.443
1q4wDQUQueuine tRNA-ribosyltransferase2.4.2.290.443
2ha6SCKAcetylcholinesterase3.1.1.70.443
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.443
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.443
2pchSAHDiphthine synthase/0.443
2r6hFADNa(+)-translocating NADH-quinone reductase subunit F/0.443
2y01Y00Beta-1 adrenergic receptor/0.443
3b03VNRIsopentenyl-diphosphate delta-isomerase/0.443
3eszFMNFlavodoxin/0.443
3jyqNADQuinate/shikimate dehydrogenase (NAD(+))/0.443
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.443
4f31KAIGlutamate receptor 3/0.443
4gtp7TPProtein farnesyltransferase subunit beta2.5.1.580.443
4jtrIBPAldo-keto reductase family 1 member C2/0.443
4nbh9CATerminal oxygenase component of carbazole/0.443
4daj0HKMuscarinic acetylcholine receptor M3/0.443
1x8lOXRRetinol dehydratase/0.442
2hxdDUPdCTP deaminase, dUMP-forming3.5.4.300.442
2owfSAHDiphthine synthase/0.442
3esyFMNFlavodoxin/0.442
3ihgVAKAklavinone 12-hydroxylase RdmE/0.442
4bfzZVZPantothenate kinase2.7.1.330.442
4fse0VABeta-secretase 13.4.23.460.442
4jtrIZPAldo-keto reductase family 1 member C2/0.442
4p9cDCMDeoxycytidylate deaminase/0.442
4wxg2BOSerine hydroxymethyltransferase/0.442
1h61PDNPentaerythritol tetranitrate reductase/0.441
1krhFADBenzoate 1,2-dioxygenase electron transfer component1.18.1.30.441
1ptjNAPNAD(P) transhydrogenase subunit beta1.6.1.20.441
1t4u81AProthrombin3.4.21.50.441
1xh7R96cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.441
2ojg19AMitogen-activated protein kinase 12.7.11.240.441
2p6lSAHDiphthine synthase/0.441
2yd0BESEndoplasmic reticulum aminopeptidase 13.4.110.441
2zevB71Geranylgeranyl pyrophosphate synthase/0.441
3c1oNAPEugenol synthase/0.441
3c27DKKProthrombin3.4.21.50.441
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.441
3eksCY9Actin-5C/0.441
4br0AU1Ectonucleoside triphosphate diphosphohydrolase 2/0.441
4cb741GPolymerase basic protein 2/0.441
4lcw1VYMajor histocompatibility complex class I-related gene protein/0.441
5kf1ACOPredicted acetyltransferase/0.441
1aquESTEstrogen sulfotransferase, testis isoform2.8.2.40.440
1cq6PY4Aspartate aminotransferase2.6.1.10.440
1dx6GNTAcetylcholinesterase3.1.1.70.440
1fwyUD1Bifunctional protein GlmU/0.440
1isgAGSADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 23.2.2.60.440
2gv8NDPThiol-specific monooxygenase1.14.130.440
2gvcFADThiol-specific monooxygenase1.14.130.440
2huxSAHDiphthine synthase/0.440
3b9oFMNAlkane monoxygenase/0.440
3hf3FMNChromate reductase/0.440
3p8hP8HLethal(3)malignant brain tumor-like protein 1/0.440
3rykTYDdTDP-4-dehydrorhamnose 3,5-epimerase/0.440
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4jzr4JREgl nine homolog 1/0.440
4l8vNAPInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.440
4mr72BVGamma-aminobutyric acid type B receptor subunit 1/0.440
4q7f3D1Uncharacterized protein/0.440
4qx5CMPcGMP-dependent protein kinase 12.7.11.120.440
4yao2AMNADPH--cytochrome P450 reductase/0.440
5erm210Fusicoccadiene synthase4.2.3.430.440