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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
1gvrTNLPentaerythritol tetranitrate reductase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1gvrTNLPentaerythritol tetranitrate reductase/1.000
1h60STRPentaerythritol tetranitrate reductase/0.705
1h62ANBPentaerythritol tetranitrate reductase/0.624
2abaSTRPentaerythritol tetranitrate reductase/0.556
3p80P80Pentaerythritol tetranitrate reductase/0.546
1h61PDNPentaerythritol tetranitrate reductase/0.533
2whqHI6Acetylcholinesterase3.1.1.70.502
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.499
3kftNADPentaerythritol tetranitrate reductase/0.495
1qtiGNTAcetylcholinesterase3.1.1.70.492
4ipw1G7Mycocyclosin synthase1.14.21.90.492
2g1s4IGRenin3.4.23.150.489
1c7oPPGHemolysin/0.488
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.485
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.485
1zgbA1EAcetylcholinesterase3.1.1.70.483
2cekN8TAcetylcholinesterase3.1.1.70.481
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.481
4q0kGA3Phytohormone-binding protein/0.480
1qx4FADNADH-cytochrome b5 reductase 31.6.2.20.477
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.476
4araC56Acetylcholinesterase3.1.1.70.476
1x1cSAHC-20 methyltransferase/0.475
2g1r3IGRenin3.4.23.150.475
4bfzZVZPantothenate kinase2.7.1.330.475
3qe2FMNNADPH--cytochrome P450 reductase/0.474
4ey6GNTAcetylcholinesterase3.1.1.70.473
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.472
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.472
1gky5GPGuanylate kinase2.7.4.80.470
2j3qTFLAcetylcholinesterase3.1.1.70.470
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.469
4ey7E20Acetylcholinesterase3.1.1.70.469
1eveE20Acetylcholinesterase3.1.1.70.468
1x1aSAMC-20 methyltransferase/0.468
2ea2F77Methionine aminopeptidase 2/0.468
3d91REMRenin3.4.23.150.468
3p8iFMNPentaerythritol tetranitrate reductase/0.468
4b7zQ4QAcetylcholinesterase3.1.1.70.468
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.467
1w6rGNTAcetylcholinesterase3.1.1.70.467
2qimZEAClass 10 plant pathogenesis-related protein/0.467
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.467
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.467
1dx6GNTAcetylcholinesterase3.1.1.70.466
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.466
2b3dFADModulator of drug activity B/0.466
2bn4FMNNADPH--cytochrome P450 reductase/0.466
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.466
1q84TZ4Acetylcholinesterase3.1.1.70.465
2xuiTZ5Acetylcholinesterase3.1.1.70.465
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.465
1odcA8BAcetylcholinesterase3.1.1.70.464
2ikuLIYRenin3.4.23.150.464
2w6cBM4Acetylcholinesterase3.1.1.70.464
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.464
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.464
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.464
1pagFMPAntiviral protein I3.2.2.220.463
2ga2A19Methionine aminopeptidase 2/0.463
3c89ARG_ARG_GLY_MET_NH2Botulinum neurotoxin type A3.4.24.690.463
2xupTZ5Acetylcholinesterase3.1.1.70.462
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.462
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.462
3qw8CYS_ARG_GLY_CYS_NH2Botulinum neurotoxin type A3.4.24.690.462
1pz0NAPProtein IolS1.1.10.461
2ha6SCKAcetylcholinesterase3.1.1.70.461
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.461
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.461
4eb7PLPCysteine desulfurase IscS 2/0.461
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.460
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.460
3q7fED2Uncharacterized protein/0.460
3qgf46FGenome polyprotein2.7.7.480.460
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.459
1x1bSAHC-20 methyltransferase/0.459
1ydaAZMCarbonic anhydrase 24.2.1.10.459
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
4uy6SAHHistidine N-alpha-methyltransferase/0.459
1h22E10Acetylcholinesterase3.1.1.70.458
1rneC60Renin3.4.23.150.458
1y1rANUUridine phosphorylase2.4.2.30.458
2ckmAA7Acetylcholinesterase3.1.1.70.458
2g1y5IGRenin3.4.23.150.458
4gddNAIUDP-galactopyranose mutase/0.458
1xh7R96cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.457
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.457
3af1GDPPantothenate kinase2.7.1.330.457
3h3qH13Collagen type IV alpha-3-binding protein/0.457
3h3r14HCollagen type IV alpha-3-binding protein/0.457
1bwsNDPGDP-L-fucose synthase/0.456
2il2LIXRenin3.4.23.150.456
3gwfNAPCyclohexanone monooxygenase/0.456
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
4ef4C2EStimulator of interferon genes protein/0.456
4ikzAFSDi-tripeptide ABC transporter (Permease)/0.456
1kh3ANPArgininosuccinate synthase/0.455
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.455
2xq0BESLeukotriene A-4 hydrolase homolog3.3.2.60.455
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.455
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.455
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.455
4j4nD44Peptidylprolyl isomerase/0.455
1vftDCSAlanine racemase/0.454
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.454
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.454
3h3t16HCollagen type IV alpha-3-binding protein/0.454
4a802ANMajor pollen allergen Bet v 1-A/0.454
4fxy0W2Neurolysin, mitochondrial3.4.24.160.454
4gd40WSLysine-specific demethylase 4A1.14.110.454
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.454
1psa0ZLPepsin A3.4.23.10.453
1r58AO5Methionine aminopeptidase 2/0.453
1u65CP0Acetylcholinesterase3.1.1.70.453
2a3cPNXEndochitinase B13.2.1.140.453
2xfyACXBeta-amylase3.2.1.20.453
4drhRAPSerine/threonine-protein kinase mTOR2.7.11.10.453
4drhRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.453
1ex75GPGuanylate kinase2.7.4.80.452
1jqdSAHHistamine N-methyltransferase2.1.1.80.452
1q23FUAChloramphenicol acetyltransferase2.3.1.280.452
1vfsDCSAlanine racemase/0.452
3wqmB29Diterpene synthase3.1.7.80.452
1kw0H4BPhenylalanine-4-hydroxylase1.14.16.10.451
1mxfMTXPutative pteridine reductase 2/0.451
1yw8A75Methionine aminopeptidase 2/0.451
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.451
4dptAGSMevalonate diphosphate decarboxylase/0.451
1r6tTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.450
1w6hTITPlasmepsin-23.4.23.390.450
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.450
2jb4A14Isopenicillin N synthase1.21.3.10.450
2jf0HBPAcetylcholinesterase3.1.1.70.450
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.450
3qj0QI3Botulinum neurotoxin type A3.4.24.690.450
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.450
4e2zJHZMethyltransferase/0.450
5jy1NADPutative short-chain dehydrogenase/reductase/0.450
1vbiNADMalate/L-lactate dehydrogenase family protein/0.449
1wk8VMSIsoleucine--tRNA ligase6.1.1.50.449
3i12ADPD-alanine--D-alanine ligase A6.3.2.40.449
3lqsPSZD-alanine aminotransferase2.6.1.210.449
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.449
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.449
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.449
3vt9YI4Vitamin D3 receptor/0.449
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.449
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.449
1i9c5ADGlutamate mutase epsilon subunit/0.448
2g247IGRenin3.4.23.150.448
2hizLIJBeta-secretase 13.4.23.460.448
2i7pACOPantothenate kinase 32.7.1.330.448
2iviACWIsopenicillin N synthase1.21.3.10.448
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.448
3djjFADGlutathione reductase, mitochondrial1.8.1.70.448
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.448
4e2wJHZMethyltransferase/0.448
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.448
2cftPLPPyridoxal phosphate phosphatase/0.447
2gv8NDPThiol-specific monooxygenase1.14.130.447
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.447
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.447
2zjuIM4Acetylcholine-binding protein/0.447
3eksCY9Actin-5C/0.447
3oagLPQRenin3.4.23.150.447
3qt62P0Mevalonate diphosphate decarboxylase/0.447
4m0f1YKAcetylcholinesterase3.1.1.70.447
4mlp2CXCryptochrome-2/0.447
4w5kPLPAspartate aminotransferase, mitochondrial/0.447
1akcPPEAspartate aminotransferase, mitochondrial2.6.1.10.446
1aquESTEstrogen sulfotransferase, testis isoform2.8.2.40.446
1qrpHH0Pepsin A-43.4.23.10.446
1votHUPAcetylcholinesterase3.1.1.70.446
2evmFC2Methionine aminopeptidase/0.446
2q92B23Methionine aminopeptidase/0.446
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.446
3qeoLLTDeoxycytidine kinase2.7.1.740.446
4na4A1RPoly(ADP-ribose) glycohydrolase3.2.1.1430.446
1hb3SCVIsopenicillin N synthase1.21.3.10.445
1ja0FMNNADPH--cytochrome P450 reductase/0.445
1qiqACCIsopenicillin N synthase1.21.3.10.445
1w4lGL8Acetylcholinesterase3.1.1.70.445
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.445
2igqSAHHistone-lysine N-methyltransferase EHMT1/0.445
2iyfERYOleandomycin glycosyltransferase2.4.10.445
2vn1FK5Peptidylprolyl isomerase/0.445
2zsaADPPantothenate kinase2.7.1.330.445
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.445
3e8xNAPBH1520 protein/0.445
3ivcFG4Pantothenate synthetase6.3.2.10.445
3p5pA3CTaxadiene synthase4.2.3.170.445
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.445
4arbC57Acetylcholinesterase3.1.1.70.445
4g8jTHMUridine phosphorylase/0.445
4lutDCSAlanine racemase/0.445
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.445
5irnADPNucleotide binding oligomerization domain containing 2/0.445
1r5gAO1Methionine aminopeptidase 2/0.444
2b4qNAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.444
2g1o2IGRenin3.4.23.150.444
2gg0U11Methionine aminopeptidase/0.444
2zr9DTPProtein RecA/0.444
3axkNDPRibulose bisphosphate carboxylase large chain4.1.1.390.444
3tr05GPGuanylate kinase/0.444
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.444
4mk828QGenome polyprotein2.7.7.480.444
4x7uZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.444
1pwyAC2Purine nucleoside phosphorylase2.4.2.10.443
1uxyEPUUDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.443
2o3uNGDADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.443
2rqfJH3Hemolymph juvenile hormone binding protein/0.443
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.443
3bk2U5PRibonuclease J/0.443
3bw4FMNPutative 2-nitropropane dioxygenase/0.443
3vilSA0Beta-glucosidase/0.443
3widNAPGlucose 1-dehydrogenase/0.443
4bf9FMNtRNA-dihydrouridine(16) synthase/0.443
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.443
4ips1G4Mycocyclosin synthase1.14.21.90.443
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.443
4psbGA3Cytokinin-specific binding protein/0.443
1ahgTYR_PLPAspartate aminotransferase2.6.1.10.442
1i59ANPChemotaxis protein CheA2.7.13.30.442
1ld7U66Protein farnesyltransferase subunit beta2.5.1.580.442
2ifaFMNUncharacterized protein/0.442
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.442
2v16C47Renin3.4.23.150.442
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.442
2xuhTZ4Acetylcholinesterase3.1.1.70.442
3abxRCBGlucanase/0.442
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.442
3c3xNAPEugenol synthase 11.1.1.3180.442
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4r81FMNPredicted NADH dehydrogenase/0.442
1b5dDCMDeoxycytidylate 5-hydroxymethyltransferase2.1.2.80.441
1h6cNDPGlucose--fructose oxidoreductase1.1.99.280.441
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.441
2bjfDXCCholoylglycine hydrolase3.5.1.240.441
2gyuHI6Acetylcholinesterase3.1.1.70.441
2xugTZ4Acetylcholinesterase3.1.1.70.441
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.441
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.441
3e6eDCSAlanine racemase/0.441
3k5c0BIBeta-secretase 13.4.23.460.441
3vydVYDRenin3.4.23.150.441
3w3lRX8Toll-like receptor 8/0.441
4bfsZVSPantothenate kinase2.7.1.330.441
4i6gFADCryptochrome-2/0.441
4jicFMNGTN Reductase/0.441
4jiq1L5GTN Reductase/0.441
4xbjIN5Alanine racemase, biosynthetic/0.441
5c80URIUridine phosphorylase/0.441
1akbPPDAspartate aminotransferase, mitochondrial2.6.1.10.440
1ja1FMNNADPH--cytochrome P450 reductase/0.440
1jedADPSulfate adenylyltransferase/0.440
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.440
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.440
2b4dCOADiamine acetyltransferase 1/0.440
2ea4F79Methionine aminopeptidase 2/0.440
2p98YE7Methionine aminopeptidase/0.440
2x06NADL-sulfolactate dehydrogenase/0.440
3g5hYTTMycocyclosin synthase1.14.21.90.440
3hlwCE3Beta-lactamase/0.440
3m30COMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.440
3m30COMMethyl-coenzyme M reductase I subunit beta2.8.4.10.440
3n0cFADFlavin-dependent thymidylate synthase2.1.1.1480.440
3ojxFMNNADPH--cytochrome P450 reductase/0.440
3q43D66M1 family aminopeptidase3.4.110.440
3t0iSAHPutative methyltransferase/0.440
3v2uATPProtein GAL3/0.440
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.440
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.440
5a0yCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.440
5a0yCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.440
4zj8SUVOrexin receptor type 1/0.440