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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
4l5aTBNS-methyl-5'-thioadenosine phosphorylase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
4l5aTBNS-methyl-5'-thioadenosine phosphorylase/1.000
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.537
3hl0NADMaleylacetate reductase/0.522
2ejzSAHDiphthine synthase/0.517
1pwyAC2Purine nucleoside phosphorylase2.4.2.10.503
3ggs2FDPurine nucleoside phosphorylase2.4.2.10.500
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.497
1jdvADNPurine nucleoside phosphorylase/0.495
1v48HA1Purine nucleoside phosphorylase2.4.2.10.495
1je1GMPPurine nucleoside phosphorylase/0.487
4eb5PLPCysteine desulfurase IscS 2/0.487
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.485
3ae4FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.484
4eb7PLPCysteine desulfurase IscS 2/0.480
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.478
2v5aLZLBiotin carboxylase6.3.4.140.478
2vq7NAPPutative flavin-containing monooxygenase/0.477
3c1kT15Prothrombin3.4.21.50.476
2a0yDIHPurine nucleoside phosphorylase2.4.2.10.475
2dxiATPGlutamate--tRNA ligase6.1.1.170.475
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.475
4yp6NAPNicotinamide-nucleotide adenylyltransferase2.7.7.10.473
4ambDUDPutative glycosyl transferase/0.472
1x1aSAMC-20 methyltransferase/0.470
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.470
4l0qNADAlcohol dehydrogenase class-3/0.470
1v35NAIEnoyl-ACP reductase/0.469
1zgv501Prothrombin3.4.21.50.469
4mv1ADPBiotin carboxylase6.3.4.140.469
1ta6177Prothrombin3.4.21.50.468
3p67FMNPentaerythritol tetranitrate reductase/0.468
3qt62P0Mevalonate diphosphate decarboxylase/0.468
2v58LZJBiotin carboxylase6.3.4.140.467
3q9bB3NAcetylpolyamine amidohydrolase/0.467
4jtqNAPAldo-keto reductase family 1 member C2/0.467
2iyfERYOleandomycin glycosyltransferase2.4.10.466
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.466
4gxs0YSGlutamate receptor 2/0.466
1culFOKAdenylate cyclase type 2/0.465
1culFOKAdenylate cyclase type 5/0.465
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
1jdtMTAPurine nucleoside phosphorylase/0.464
1lv89PPPurine nucleoside phosphorylase2.4.2.10.464
1yryMSGPurine nucleoside phosphorylase2.4.2.10.464
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.463
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.462
1lvu9PPPurine nucleoside phosphorylase2.4.2.10.462
1s7gNADNAD-dependent protein deacylase 2/0.462
1v453DGPurine nucleoside phosphorylase2.4.2.10.462
4e7r0NWProthrombin3.4.21.50.462
2gjlFMNNitronate monooxygenase1.13.12.160.461
3c35KAIGlutamate receptor ionotropic, kainate 1/0.461
1d4pBPPProthrombin3.4.21.50.460
1rfgGMPPurine nucleoside phosphorylase2.4.2.10.460
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.460
2r2mI50Prothrombin3.4.21.50.460
2xlpNAPPutative flavin-containing monooxygenase/0.460
1fxuGU7Purine nucleoside phosphorylase2.4.2.10.459
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.459
1ja0FMNNADPH--cytochrome P450 reductase/0.459
1mbbEEBUDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.459
3h3r14HCollagen type IV alpha-3-binding protein/0.459
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.459
4jayNAPUDP-N-acetylenolpyruvoylglucosamine reductase/0.459
1bk0ACVIsopenicillin N synthase1.21.3.10.458
2ikuLIYRenin3.4.23.150.458
2zvbSAHPrecorrin-3 C17-methyltransferase/0.458
3h3sH15Collagen type IV alpha-3-binding protein/0.458
3zeiAWHO-acetylserine sulfhydrylase/0.458
4zwmPLPOrnithine aminotransferase, mitochondrial, putative/0.458
1h63FMNPentaerythritol tetranitrate reductase/0.457
4bfxZVXPantothenate kinase2.7.1.330.457
4twrNADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase/0.457
1h60STRPentaerythritol tetranitrate reductase/0.456
1zgi382Prothrombin3.4.21.50.456
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.456
2zfr46UProthrombin3.4.21.50.456
3h3qH13Collagen type IV alpha-3-binding protein/0.456
3zcsCAWGlycogen phosphorylase, muscle form2.4.1.10.456
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.455
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.455
4lnbED5CaaX farnesyltransferase beta subunit Ram1/0.455
1jdzFMBPurine nucleoside phosphorylase/0.454
2gv8NDPThiol-specific monooxygenase1.14.130.454
3pm1ETHTH-type transcriptional regulator QacR/0.454
4awtFMNNADH:flavin oxidoreductase Sye1/0.454
4imfSI3N-acetylneuraminate lyase/0.454
1owe675Urokinase-type plasminogen activator3.4.21.730.453
2iko7IGRenin3.4.23.150.453
3hlwCE3Beta-lactamase/0.453
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.453
3vilSA0Beta-glucosidase/0.453
4ycpFMNtRNA-dihydrouridine(16) synthase/0.453
1w6hTITPlasmepsin-23.4.23.390.452
1yqsBSAD-alanyl-D-alanine carboxypeptidase3.4.16.40.452
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.452
2aj4ANPGalactokinase2.7.1.60.452
2v59LZKBiotin carboxylase6.3.4.140.452
5dozNDPJamJ/0.452
1fmlRTLRetinol dehydratase/0.451
2g247IGRenin3.4.23.150.451
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.451
3cluFADElectron transfer flavoprotein subunit alpha/0.451
3mauEXTPutative sphingosine-1-phosphate lyase/0.451
4f7iNAD3-isopropylmalate dehydrogenase1.1.1.850.451
4u8iFDAUDP-galactopyranose mutase/0.451
4xbjIN5Alanine racemase, biosynthetic/0.451
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
2a9y26AAdenosine kinase2.7.1.200.450
2c20NADUDP-glucose 4-epimerase/0.450
2gevCOKPantothenate kinase2.7.1.330.450
2vkeTACTetracycline repressor protein class D/0.450
3b9xNOSPyrimidine-specific ribonucleoside hydrolase RihB3.2.2.80.450
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.450
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.450
3wquATPCell division protein FtsA/0.450
4bftZVTPantothenate kinase2.7.1.330.450
4brdANPEctonucleoside triphosphate diphosphohydrolase I/0.450
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.449
1qrtATPGlutamine--tRNA ligase6.1.1.180.449
2g1n1IGRenin3.4.23.150.449
2ifaFMNUncharacterized protein/0.449
2vqbNAPPutative flavin-containing monooxygenase/0.449
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.449
3wqtANPCell division protein FtsA/0.449
4du82P0Mevalonate diphosphate decarboxylase/0.449
1h65GDPTranslocase of chloroplast 343.6.50.448
1z7yAA5Cysteine synthase 12.5.1.470.448
2q1tNADPutative nucleotide sugar epimerase/ dehydratase/0.448
3qe2FMNNADPH--cytochrome P450 reductase/0.448
4frkDWDBeta-secretase 13.4.23.460.448
4rn615UProthrombin3.4.21.50.448
4y1bNAPAntE/0.448
4y9uNAPNADPH--cytochrome P450 reductase/0.448
1d3pBT3Prothrombin3.4.21.50.447
1me6IVSPlasmepsin-23.4.23.390.447
1mvtDTMDihydrofolate reductase1.5.1.30.447
2cekN8TAcetylcholinesterase3.1.1.70.447
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.447
3br3ETHTH-type transcriptional regulator QacR/0.447
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.447
3h06VBPGlutamate receptor 2/0.447
3in6FMNUncharacterized protein/0.447
3ojwFMNNADPH--cytochrome P450 reductase/0.447
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.447
4mqt2CUMuscarinic acetylcholine receptor M2/0.447
1wxjIPLTryptophan synthase alpha chain/0.446
2b3dFADModulator of drug activity B/0.446
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.446
2ggsNDPdTDP-4-dehydrorhamnose reductase/0.446
2xvhNAPPutative flavin-containing monooxygenase/0.446
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3eq02TSProthrombin3.4.21.50.446
4b1rITCTetracycline repressor protein class D/0.446
4bfsZVSPantothenate kinase2.7.1.330.446
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.446
4hn1TYDdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.446
1bim0QBRenin3.4.23.150.445
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.445
1qorNDPQuinone oxidoreductase 1/0.445
2bsxNOSPurine nucleoside phosphorylase/0.445
2w6zL21Biotin carboxylase6.3.4.140.445
2whqHI6Acetylcholinesterase3.1.1.70.445
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.445
3fhxPLPPyridoxal kinase2.7.1.350.445
3ohh3HHBeta-secretase 13.4.23.460.445
3vg10GTBeta-secretase 13.4.23.460.445
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.445
4bfzZVZPantothenate kinase2.7.1.330.445
4de10J6Beta-lactamase/0.445
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.445
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.445
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.445
4k36SAMAnaerobic sulfatase-maturating enzyme1.8.980.445
4pjkADPMyosin-2 heavy chain/0.445
4rvfTYDD-mycarose 3-C-methyltransferase/0.445
4to5DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.445
1cbfSAHCobalt-precorrin-4 C(11)-methyltransferase2.1.1.2710.444
1e2nRCAThymidine kinase/0.444
1h50FMNPentaerythritol tetranitrate reductase/0.444
1pf7IMHPurine nucleoside phosphorylase2.4.2.10.444
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.444
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.444
2rlcCHDCholoylglycine hydrolase3.5.1.240.444
2xlrFADPutative flavin-containing monooxygenase/0.444
2xlrNAPPutative flavin-containing monooxygenase/0.444
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3k8q22APurine nucleoside phosphorylase2.4.2.10.444
3mauPLRPutative sphingosine-1-phosphate lyase/0.444
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.444
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.444
4cf6CBDNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
4gddNAIUDP-galactopyranose mutase/0.444
4q0kGA3Phytohormone-binding protein/0.444
5f54TMPSingle-stranded-DNA-specific exonuclease/0.444
1odcA8BAcetylcholinesterase3.1.1.70.443
1w6rGNTAcetylcholinesterase3.1.1.70.443
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.443
2bf4FMNNADPH--cytochrome P450 reductase/0.443
2dshSAHDiphthine synthase/0.443
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.443
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3p74FMNPentaerythritol tetranitrate reductase/0.443
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.443
4b65NDPL-ornithine N(5)-monooxygenase/0.443
4bfuZVUPantothenate kinase2.7.1.330.443
4g3jVNTLanosterol 14-alpha-demethylase/0.443
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.443
4j7hTRHPCZA361.3/0.443
4k38SAMAnaerobic sulfatase-maturating enzyme1.8.980.443
4kniE1ECarbonic anhydrase 24.2.1.10.443
4yaf2AMNADPH--cytochrome P450 reductase/0.443
4yagNAIC alpha-dehydrogenase/0.443
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.443
5fm7ADPRuvB-like helicase/0.443
4zj8SUVOrexin receptor type 1/0.443
1d3dBZTProthrombin3.4.21.50.442
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.442
1icsFMN12-oxophytodienoate reductase 11.3.1.420.442
1pl6572Sorbitol dehydrogenase1.1.1.140.442
2g1r3IGRenin3.4.23.150.442
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.442
2xvfFADPutative flavin-containing monooxygenase/0.442
2xviFADPutative flavin-containing monooxygenase/0.442
3c27DKKProthrombin3.4.21.50.442
3h3t16HCollagen type IV alpha-3-binding protein/0.442
3nsh957Beta-secretase 13.4.23.460.442
4an4DUDPutative glycosyl transferase/0.442
4h0vNADIota toxin component Ia/0.442
4i0i957Beta-secretase 13.4.23.460.442
4mr72BVGamma-aminobutyric acid type B receptor subunit 1/0.442
5e5h0T1Succinyl-CoA:acetate CoA-transferase/0.442
1ascNPLAspartate aminotransferase2.6.1.10.441
1h51FMNPentaerythritol tetranitrate reductase/0.441
1p0pBCHCholinesterase3.1.1.80.441
2a0wDIHPurine nucleoside phosphorylase2.4.2.10.441
2h21SAMRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.441
2iviACWIsopenicillin N synthase1.21.3.10.441
2vbdV10Isopenicillin N synthase1.21.3.10.441
2xy93ESAngiotensin-converting enzyme3.2.10.441
3ho9N3A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.441
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.441
1obnASVIsopenicillin N synthase1.21.3.10.440
1pq944BOxysterols receptor LXR-beta/0.440
1r6uTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.440
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.440
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
2ixkTDOdTDP-4-dehydrorhamnose 3,5-epimerase5.1.3.130.440
2vuuNAPNitrogen metabolite repression protein nmrA/0.440
2xuiTZ5Acetylcholinesterase3.1.1.70.440
3f03FMNPentaerythritol tetranitrate reductase/0.440
3lsiFADPyranose 2-oxidase/0.440
3q43D66M1 family aminopeptidase3.4.110.440
3r95ACOMccE protein/0.440
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.440
4kbyC2EStimulator of interferon genes protein/0.440
4m83ERYOleandomycin glycosyltransferase2.4.10.440
4x7zZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.440
5f8eSAHPossible transcriptional regulatory protein/0.440
4s0vSUVOrexin receptor type 2/0.440