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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
2evcFC3Methionine aminopeptidase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2evcFC3Methionine aminopeptidase/1.000
2evmFC2Methionine aminopeptidase/0.891
2q94A04Methionine aminopeptidase/0.773
2q92B23Methionine aminopeptidase/0.738
1xnzFCDMethionine aminopeptidase/0.705
2gg8U15Methionine aminopeptidase/0.682
3iu7FCDMethionine aminopeptidase 2/0.675
2q93B21Methionine aminopeptidase/0.668
2p98YE7Methionine aminopeptidase/0.651
3iu8T03Methionine aminopeptidase 2/0.648
3pkeY10Methionine aminopeptidase 2/0.646
2gg9U16Methionine aminopeptidase/0.641
2q96A18Methionine aminopeptidase/0.639
2ggbU17Methionine aminopeptidase/0.636
2p99YE6Methionine aminopeptidase/0.625
2gg0U11Methionine aminopeptidase/0.621
2gg2U12Methionine aminopeptidase/0.612
3d27W29Methionine aminopeptidase/0.601
4iktTFVMethionine aminopeptidase 1/0.600
4ikuSHXMethionine aminopeptidase 1/0.599
3pkbY16Methionine aminopeptidase 2/0.597
4flkY10Methionine aminopeptidase 1/0.597
2g6pHM2Methionine aminopeptidase 1/0.594
4fliY16Methionine aminopeptidase 1/0.590
3pkdY10Methionine aminopeptidase 2/0.588
3pkaY02Methionine aminopeptidase 2/0.571
4iksTFDMethionine aminopeptidase 1/0.570
1r5gAO1Methionine aminopeptidase 2/0.569
4hxx1AYMethionine aminopeptidase 1/0.565
1c23MPHMethionine aminopeptidase/0.564
2nq7HM5Methionine aminopeptidase 1/0.557
4ikrPVPMethionine aminopeptidase 1/0.557
2gg3U13Methionine aminopeptidase/0.556
4fllYZ6Methionine aminopeptidase 1/0.545
3pkcY08Methionine aminopeptidase 2/0.540
4fljY08Methionine aminopeptidase 1/0.520
2oazI96Methionine aminopeptidase 2/0.511
2ga2A19Methionine aminopeptidase 2/0.506
3iu9T07Methionine aminopeptidase 2/0.502
2ea4F79Methionine aminopeptidase 2/0.501
1qzyTDEMethionine aminopeptidase 2/0.496
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.495
1r5hAO2Methionine aminopeptidase 2/0.494
1zgbA1EAcetylcholinesterase3.1.1.70.494
3wqmB29Diterpene synthase3.1.7.80.494
2xupTZ5Acetylcholinesterase3.1.1.70.493
2vd7PD2Lysine-specific demethylase 4A1.14.110.491
1yw9A84Methionine aminopeptidase 2/0.489
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.488
2pb1NFGGlucan 1,3-beta-glucosidase/0.487
1yw7A41Methionine aminopeptidase 2/0.485
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.483
4gd40WSLysine-specific demethylase 4A1.14.110.483
2ea2F77Methionine aminopeptidase 2/0.482
2j3qTFLAcetylcholinesterase3.1.1.70.482
4ey7E20Acetylcholinesterase3.1.1.70.482
1eveE20Acetylcholinesterase3.1.1.70.481
1r58AO5Methionine aminopeptidase 2/0.480
1yw8A75Methionine aminopeptidase 2/0.480
1tllFMNNitric oxide synthase, brain1.14.13.390.478
1icqOPD12-oxophytodienoate reductase 11.3.1.420.477
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.477
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.477
3mj4URMUDP-galactopyranose mutase/0.476
4d6qPD2Lysine-specific demethylase 4D1.14.110.475
2xukTZ5Acetylcholinesterase3.1.1.70.474
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.474
1t7o152Carnitine O-acetyltransferase2.3.1.70.473
2xugTZ4Acetylcholinesterase3.1.1.70.473
2cekN8TAcetylcholinesterase3.1.1.70.472
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.472
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.470
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.469
2xuiTZ5Acetylcholinesterase3.1.1.70.469
1odcA8BAcetylcholinesterase3.1.1.70.468
4lxlPD2Lysine-specific demethylase 4B1.14.110.468
1ex75GPGuanylate kinase2.7.4.80.467
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.466
1vkgCRIHistone deacetylase 83.5.1.980.465
2aouCQAHistamine N-methyltransferase2.1.1.80.465
2jf0HBPAcetylcholinesterase3.1.1.70.465
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.465
2xujTZ5Acetylcholinesterase3.1.1.70.465
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.465
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.465
1amoFMNNADPH--cytochrome P450 reductase/0.464
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.463
2gywOBIAcetylcholinesterase3.1.1.70.463
2w6cBM4Acetylcholinesterase3.1.1.70.463
4m0f1YKAcetylcholinesterase3.1.1.70.463
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.462
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
4nv14TGFormyl transferase/0.462
2xuoTZ4Acetylcholinesterase3.1.1.70.461
4b7zQ4QAcetylcholinesterase3.1.1.70.461
4q7f3D1Uncharacterized protein/0.460
2aot2PMHistamine N-methyltransferase2.1.1.80.459
2jl1NAPTriphenylmethane reductase/0.459
3cavCI23-oxo-5-beta-steroid 4-dehydrogenase/0.459
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.459
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.458
4zwpM44Xaa-Pro dipeptidase3.4.13.90.458
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.457
4rxrDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.457
1u65CP0Acetylcholinesterase3.1.1.70.456
2ha6SCKAcetylcholinesterase3.1.1.70.456
1kyvRBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.455
1q84TZ4Acetylcholinesterase3.1.1.70.455
2g1r3IGRenin3.4.23.150.455
3c3xNAPEugenol synthase 11.1.1.3180.455
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3zv7NHGAcetylcholinesterase3.1.1.70.455
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.455
4nv10FXFormyl transferase/0.455
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.454
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.454
1h22E10Acetylcholinesterase3.1.1.70.453
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
2qimZEAClass 10 plant pathogenesis-related protein/0.453
3aezGDPPantothenate kinase2.7.1.330.453
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.453
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.453
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.453
3vf2ADPnebramycin 5' synthase6.1.2.20.452
1w4lGL8Acetylcholinesterase3.1.1.70.451
2g247IGRenin3.4.23.150.451
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.451
3af1GDPPantothenate kinase2.7.1.330.451
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.451
3ojwFMNNADPH--cytochrome P450 reductase/0.451
3ziuLSSLeucyl-tRNA synthetase/0.451
4ey6GNTAcetylcholinesterase3.1.1.70.451
4mlp2CXCryptochrome-2/0.451
2gv8NDPThiol-specific monooxygenase1.14.130.450
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.450
3uzxAOM3-oxo-5-beta-steroid 4-dehydrogenase/0.450
2whqHI6Acetylcholinesterase3.1.1.70.449
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.449
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.449
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.449
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.449
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4mr72BVGamma-aminobutyric acid type B receptor subunit 1/0.449
4to0DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.449
1c4vIH2Prothrombin3.4.21.50.448
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
2g1o2IGRenin3.4.23.150.448
2il2LIXRenin3.4.23.150.448
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.448
5c1mCLRMu-type opioid receptor/0.448
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.447
1nsgRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.447
1nsgRADSerine/threonine-protein kinase mTOR2.7.11.10.447
2dg4RAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.447
2xi4AFTAcetylcholinesterase3.1.1.70.447
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.447
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.447
1qtiGNTAcetylcholinesterase3.1.1.70.446
2g263LGRenin3.4.23.150.446
2v9cMREFMN-dependent NADH-azoreductase 1/0.446
2xuhTZ4Acetylcholinesterase3.1.1.70.446
2xuqTZ4Acetylcholinesterase3.1.1.70.446
4a87NARMajor pollen allergen Bet v 1-A/0.446
5iefNBVNeutral alpha-glucosidase AB3.2.1.840.446
1i9c5ADGlutamate mutase epsilon subunit/0.445
2g226IGRenin3.4.23.150.445
2v16C47Renin3.4.23.150.445
2xveFADPutative flavin-containing monooxygenase/0.445
2zbwFADFerredoxin--NADP reductase/0.445
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.445
3v2uATPProtein GAL3/0.445
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.445
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.444
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.444
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.444
2xq0BESLeukotriene A-4 hydrolase homolog3.3.2.60.444
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3o5rFK5Peptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.444
3pdqKC6Lysine-specific demethylase 4A1.14.110.444
3q43D66M1 family aminopeptidase3.4.110.444
3qe2FMNNADPH--cytochrome P450 reductase/0.444
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.444
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.443
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.443
1u1gBBBUridine phosphorylase2.4.2.30.443
1ut6A8NAcetylcholinesterase3.1.1.70.443
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.443
2x91LPRAngiotensin-converting enzyme3.4.15.10.443
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.443
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3l7gM44Xaa-Pro dipeptidase3.4.13.90.443
3lzwNAPFerredoxin--NADP reductase 21.18.1.20.443
4bis8HQLysine-specific demethylase 4A1.14.110.443
4jt91NSNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.443
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.443
1ro6ROLcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.442
1vhzAPRADP compounds hydrolase NudE3.6.10.442
2xnvVU3Soluble acetylcholine receptor/0.442
2xufTZ4Acetylcholinesterase3.1.1.70.442
3caqNDP3-oxo-5-beta-steroid 4-dehydrogenase/0.442
1c4uIH1Prothrombin3.4.21.50.441
1o2g696Prothrombin3.4.21.50.441
2po3T4K4-dehydrase/0.441
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.441
3qbjNXZDipeptidyl peptidase 4/0.441
3v0m5GWHisto-blood group ABO system transferase/0.441
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.441
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.441
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.441
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.441
4u163C0Muscarinic acetylcholine receptor M3/0.441
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.440
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.440
3af3GCPPantothenate kinase2.7.1.330.440
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.440