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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
1dfoPLGSerine hydroxymethyltransferase2.1.2.1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1dfoPLGSerine hydroxymethyltransferase2.1.2.11.000
4wxg2BOSerine hydroxymethyltransferase/0.601
4wxfPLGSerine hydroxymethyltransferase/0.531
3fhxPLPPyridoxal kinase2.7.1.350.496
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.494
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.490
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.486
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.484
4eb5PLPCysteine desulfurase IscS 2/0.483
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.480
1u1gBBBUridine phosphorylase2.4.2.30.479
2bb3SAHCobalamin biosynthesis precorrin-6Y methylase (CbiE)/0.479
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.479
2ilvC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.478
1oxoIK2Aspartate aminotransferase, mitochondrial2.6.1.10.475
4bfvZVVPantothenate kinase2.7.1.330.474
2a94AP0L-lactate dehydrogenase1.1.1.270.471
1g1aNADdTDP-glucose 4,6-dehydratase/0.470
4brgGNPEctonucleoside triphosphate diphosphohydrolase I/0.470
1obnASVIsopenicillin N synthase1.21.3.10.469
5er0FADUncharacterized NAD(FAD)-dependent dehydrogenase/0.469
3fhxPXLPyridoxal kinase2.7.1.350.468
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.467
4ge90L0Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.467
1ja0FADNADPH--cytochrome P450 reductase/0.466
3wquATPCell division protein FtsA/0.466
4xbjIN5Alanine racemase, biosynthetic/0.466
1ppjANYCytochrome b/0.465
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.465
3q43D66M1 family aminopeptidase3.4.110.465
2c29NAPDihydroflavonol 4-reductase/0.464
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.464
2g226IGRenin3.4.23.150.463
3lpkZ76Beta-secretase 13.4.23.460.463
3lqfNADGalactitol dehydrogenase/0.463
3phiNDPShikimate dehydrogenase (NADP(+))/0.463
1u1f183Uridine phosphorylase2.4.2.30.462
3gncQQQGlutaryl-CoA dehydrogenase/0.462
4eb7PLPCysteine desulfurase IscS 2/0.462
1dgmADNAdenosine kinase2.7.1.200.461
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.461
2g8yNADHydroxycarboxylate dehydrogenase B/0.460
2rlcCHDCholoylglycine hydrolase3.5.1.240.460
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.459
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.459
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.459
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.459
2ffqGSPRas-related protein Rab-6B/0.459
3b6pTMPThree-prime repair exonuclease 13.1.11.20.459
4bfwZVWPantothenate kinase2.7.1.330.459
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.458
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.458
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.458
1c7oPPGHemolysin/0.457
1wur8DGGTP cyclohydrolase 1/0.457
2ex1C5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.457
2g1r3IGRenin3.4.23.150.457
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.457
4psbGA3Cytokinin-specific binding protein/0.457
2hp2KE4Glutamate-1-semialdehyde 2,1-aminomutase5.4.3.80.456
3aezGDPPantothenate kinase2.7.1.330.456
3v0p4GWHisto-blood group ABO system transferase/0.456
4ambDUDPutative glycosyl transferase/0.456
1nbiSAMGlycine N-methyltransferase2.1.1.200.455
2g1s4IGRenin3.4.23.150.455
3wagTYDGlycosyltransferase/0.455
3wqmB29Diterpene synthase3.1.7.80.455
5ah5LSSLeucine--tRNA ligase/0.455
1h73ANPHomoserine kinase2.7.1.390.454
1szgFNSCytochrome b2, mitochondrial1.1.2.30.454
1xdpATPPolyphosphate kinase/0.454
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.454
2pj4414Carboxypeptidase B/0.454
3br3ETHTH-type transcriptional regulator QacR/0.454
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.454
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.454
3e6eDCSAlanine racemase/0.454
3qlsNDPDihydrofolate reductase1.5.1.30.454
3b70NAPEnoyl reductase LovC10.453
3bgxTMPThymidylate synthase/0.453
4bfzZVZPantothenate kinase2.7.1.330.453
1me6IVSPlasmepsin-23.4.23.390.452
1n4pCYS_VAL_ILE_LEU_GERGeranylgeranyl transferase type-1 subunit beta2.5.1.590.452
1t2cNAIL-lactate dehydrogenase1.1.1.270.452
1vzbUMPThymidylate synthase/0.452
2ikuLIYRenin3.4.23.150.452
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.452
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.452
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.452
4mr72BVGamma-aminobutyric acid type B receptor subunit 1/0.452
4pzsACOHistone acetyltransferase p300/0.452
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.451
1lwiNAP3-alpha-hydroxysteroid dehydrogenase1.1.1.500.451
2ag5NAD3-hydroxybutyrate dehydrogenase type 2/0.451
2b58COADiamine acetyltransferase 1/0.451
2b8l5HABeta-secretase 13.4.23.460.451
3gwdFADCyclohexanone monooxygenase/0.451
3hyoADPPyridoxal kinase/0.451
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.451
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.451
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.451
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.451
3v2uATPProtein GAL3/0.451
4e32DWNMethyltransferase/0.451
4jayNAPUDP-N-acetylenolpyruvoylglucosamine reductase/0.451
4lutDCSAlanine racemase/0.451
5kwvANPPantothenate synthetase/0.451
4xnw2IDP2Y purinoceptor 1/0.451
2f6rACOBifunctional coenzyme A synthase/0.450
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.450
3b1dPLSBetaC-S lyase/0.450
3i0oSMISpectinomycin phosphotransferase/0.450
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.450
4ef4C2EStimulator of interferon genes protein/0.450
4oztP1AEcdysone receptor, putative/0.450
1bim0QBRenin3.4.23.150.449
1f8fNADBenzyl alcohol dehydrogenase/0.449
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.449
1w6hTITPlasmepsin-23.4.23.390.449
2g247IGRenin3.4.23.150.449
2i7nACOPantothenate kinase 12.7.1.330.449
2jgsBTNAvidin/0.449
2p83MR0Beta-secretase 13.4.23.460.449
3d3wNAPL-xylulose reductase1.1.1.100.449
3elePLPAminotransferase/0.449
5jqhCAUBeta-2 adrenergic receptor/0.449
1jueFMNDihydroorotate dehydrogenase A (fumarate)1.3.98.10.448
2g1y5IGRenin3.4.23.150.448
3tfyMET_LEU_GLY_PRON-alpha-acetyltransferase 502.3.10.448
4drn0MCPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.448
4exg916Beta-secretase 13.4.23.460.448
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.448
4m83ERYOleandomycin glycosyltransferase2.4.10.448
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.448
4xr9NADCalS8/0.448
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.447
2gevCOKPantothenate kinase2.7.1.330.447
2gv8NDPThiol-specific monooxygenase1.14.130.447
3ai0PNWBeta-glucosidase/0.447
3imgBZ3Pantothenate synthetase6.3.2.10.447
3lqsPSZD-alanine aminotransferase2.6.1.210.447
3ndjJHZMethyltransferase/0.447
3qt62P0Mevalonate diphosphate decarboxylase/0.447
3zbsOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.447
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
4fhd0TTSpore photoproduct lyase/0.447
5e5h0T1Succinyl-CoA:acetate CoA-transferase/0.447
1j9zFADNADPH--cytochrome P450 reductase/0.446
1p0hACOMycothiol acetyltransferase2.3.1.1890.446
2ylzFADPhenylacetone monooxygenase1.14.13.920.446
2z95NDPGDP-mannose 4,6-dehydratase/0.446
3gqvNAPEnoyl reductase LovC10.446
3hl0NADMaleylacetate reductase/0.446
4egbNADdTDP-glucose 4,6-dehydratase/0.446
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.446
5c1d12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.446
1ds7FMNOxygen-insensitive NAD(P)H nitroreductase/0.445
1rp7TZDPyruvate dehydrogenase E1 component1.2.4.10.445
1w19T5P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.445
1xddAAYIntegrin alpha-L/0.445
1xseNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
2gjlFMNNitronate monooxygenase1.13.12.160.445
2he5NDPAldo-keto reductase family 1 member C211.1.10.445
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.445
3h3t16HCollagen type IV alpha-3-binding protein/0.445
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4blrUTPNTPase P4/0.445
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.445
4g3jVNTLanosterol 14-alpha-demethylase/0.445
4jtqNAPAldo-keto reductase family 1 member C2/0.445
1bk0ACVIsopenicillin N synthase1.21.3.10.444
1hb1OCVIsopenicillin N synthase1.21.3.10.444
1kqnNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.444
1x1bSAHC-20 methyltransferase/0.444
1x1dSAHC-20 methyltransferase/0.444
1z41FMNNADPH dehydrogenase/0.444
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.444
2ed4NAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.444
2fxuBIDActin, alpha skeletal muscle/0.444
2vyqFADFerredoxin--NADP reductase1.18.1.20.444
2wmdZZ0NmrA-like family domain-containing protein 1/0.444
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3jzdNADMaleylacetate reductase/0.444
3kmyD8YBeta-secretase 13.4.23.460.444
3nsh957Beta-secretase 13.4.23.460.444
3sufSUEPolyprotein/0.444
3zoiM2WIsopenicillin N synthase1.21.3.10.444
4a6rTA8Probable aminotransferase/0.444
4bftZVTPantothenate kinase2.7.1.330.444
4du6GTPGTP cyclohydrolase 1/0.444
4g7gVFVLanosterol 14-alpha-demethylase/0.444
4i0i957Beta-secretase 13.4.23.460.444
4qxaGTPRas-related protein Rab-9A/0.444
5jsfNAD17-beta-hydroxysteroid dehydrogenase 141.1.10.444
1j36LPRAngiotensin-converting enzyme3.4.15.10.443
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.443
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.443
1qrpHH0Pepsin A-43.4.23.10.443
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
2c20NADUDP-glucose 4-epimerase/0.443
2jb4A14Isopenicillin N synthase1.21.3.10.443
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3c8bARG_ARG_GLY_ILE_NH2Botulinum neurotoxin type A3.4.24.690.443
3d91REMRenin3.4.23.150.443
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.443
3pqbVGPPutative oxidoreductase/0.443
4hh4SAHCcbJ/0.443
4j0v1H7Beta-secretase 13.4.23.460.443
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.443
4uugPXGBranched-chain amino acid aminotransferase, putative/0.443
3vw7VPXProteinase-activated receptor 1/0.443
1cscCMCCitrate synthase, mitochondrial2.3.3.10.442
2bjfDXCCholoylglycine hydrolase3.5.1.240.442
2cndFADNitrate reductase [NADH]1.7.1.10.442
2ebaFADPutative glutaryl-CoA dehydrogenase/0.442
2futH1SHeparin and heparin-sulfate lyase/0.442
2g1n1IGRenin3.4.23.150.442
2hfuMEVMevalonate kinase/0.442
2irzI02Beta-secretase 13.4.23.460.442
3duyAFJBeta-secretase 13.4.23.460.442
3fktSIIBeta-secretase 13.4.23.460.442
3iocA5DPantothenate synthetase6.3.2.10.442
3o0qADNVitamin B12-dependent ribonucleotide reductase/0.442
3ohf3HFBeta-secretase 13.4.23.460.442
4an4DUDPutative glycosyl transferase/0.442
4b1rITCTetracycline repressor protein class D/0.442
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.442
4kp8E1GCarbonic anhydrase 124.2.1.10.442
4mlp2CXCryptochrome-2/0.442
1odcA8BAcetylcholinesterase3.1.1.70.441
1qtiGNTAcetylcholinesterase3.1.1.70.441
1udaUFGUDP-glucose 4-epimerase5.1.3.20.441
1vzaUMPThymidylate synthase/0.441
2gilGTPRas-related protein Rab-6A/0.441
2gr1FADFerredoxin reductase/0.441
2iviACWIsopenicillin N synthase1.21.3.10.441
2ou2ACOHistone acetyltransferase KAT5/0.441
2qbuSAHPrecorrin-2 methyltransferase/0.441
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.441
3eksCY9Actin-5C/0.441
3gwfNAPCyclohexanone monooxygenase/0.441
3kpbSAMUncharacterized protein MJ0100/0.441
4f9gC2EStimulator of interferon genes protein/0.441
4itxIN5Cystathionine beta-lyase MetC4.4.1.80.441
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.441
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.441
4k6fNAPPutative Acetoacetyl-CoA reductase/0.441
4l1xNAPAldo-keto reductase family 1 member C2/0.441
4mr92BXGamma-aminobutyric acid type B receptor subunit 1/0.441
4rvfTYDD-mycarose 3-C-methyltransferase/0.441
1gvrTNLPentaerythritol tetranitrate reductase/0.440
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
2fdpFRPBeta-secretase 13.4.23.460.440
2gesCOKPantothenate kinase2.7.1.330.440
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.440
2p4j23IBeta-secretase 13.4.23.460.440
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.440
2y0mACOHistone acetyltransferase KAT8/0.440
2zcvNDPQuinone oxidoreductase 21.6.5.20.440
3daaPDDD-alanine aminotransferase2.6.1.210.440
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3h3r14HCollagen type IV alpha-3-binding protein/0.440
3isjA8DPantothenate synthetase6.3.2.10.440
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4de00JBBeta-lactamase/0.440
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.440
4i9n1E5L-lactate dehydrogenase A chain1.1.1.270.440
5a0yCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.440
5a0yCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.440