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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
2ggbU17Methionine aminopeptidase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2ggbU17Methionine aminopeptidase/1.000
2gg0U11Methionine aminopeptidase/0.660
2gg8U15Methionine aminopeptidase/0.654
2evcFC3Methionine aminopeptidase/0.635
2evmFC2Methionine aminopeptidase/0.630
2q92B23Methionine aminopeptidase/0.626
2q94A04Methionine aminopeptidase/0.622
3pkeY10Methionine aminopeptidase 2/0.622
2gg3U13Methionine aminopeptidase/0.609
2gg9U16Methionine aminopeptidase/0.608
2p98YE7Methionine aminopeptidase/0.608
3iu7FCDMethionine aminopeptidase 2/0.602
3iu8T03Methionine aminopeptidase 2/0.596
2q93B21Methionine aminopeptidase/0.594
3d27W29Methionine aminopeptidase/0.585
4iksTFDMethionine aminopeptidase 1/0.585
2q96A18Methionine aminopeptidase/0.583
4iktTFVMethionine aminopeptidase 1/0.579
3pkdY10Methionine aminopeptidase 2/0.573
2nq7HM5Methionine aminopeptidase 1/0.571
3pkaY02Methionine aminopeptidase 2/0.569
2gg2U12Methionine aminopeptidase/0.568
1xnzFCDMethionine aminopeptidase/0.561
2p99YE6Methionine aminopeptidase/0.557
4hxx1AYMethionine aminopeptidase 1/0.550
3pkbY16Methionine aminopeptidase 2/0.548
4ikrPVPMethionine aminopeptidase 1/0.548
2g6pHM2Methionine aminopeptidase 1/0.547
4ikuSHXMethionine aminopeptidase 1/0.543
4fllYZ6Methionine aminopeptidase 1/0.535
1c23MPHMethionine aminopeptidase/0.534
4flkY10Methionine aminopeptidase 1/0.534
4fliY16Methionine aminopeptidase 1/0.518
4q7f3D1Uncharacterized protein/0.511
3pkcY08Methionine aminopeptidase 2/0.508
1r5gAO1Methionine aminopeptidase 2/0.492
2xukTZ5Acetylcholinesterase3.1.1.70.490
2xuoTZ4Acetylcholinesterase3.1.1.70.490
4fljY08Methionine aminopeptidase 1/0.490
1r58AO5Methionine aminopeptidase 2/0.486
1eveE20Acetylcholinesterase3.1.1.70.482
2w6cBM4Acetylcholinesterase3.1.1.70.482
1yw8A75Methionine aminopeptidase 2/0.481
4ey7E20Acetylcholinesterase3.1.1.70.481
2xugTZ4Acetylcholinesterase3.1.1.70.479
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.478
3iu9T07Methionine aminopeptidase 2/0.478
1odcA8BAcetylcholinesterase3.1.1.70.477
2cekN8TAcetylcholinesterase3.1.1.70.477
2jf0HBPAcetylcholinesterase3.1.1.70.477
2ga2A19Methionine aminopeptidase 2/0.476
1q84TZ4Acetylcholinesterase3.1.1.70.475
1w4lGL8Acetylcholinesterase3.1.1.70.475
2ha6SCKAcetylcholinesterase3.1.1.70.475
2aouCQAHistamine N-methyltransferase2.1.1.80.472
2xuiTZ5Acetylcholinesterase3.1.1.70.471
2xuqTZ4Acetylcholinesterase3.1.1.70.471
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.471
2wzySQXSoluble acetylcholine receptor/0.468
4m0f1YKAcetylcholinesterase3.1.1.70.468
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.467
3ziuLSSLeucyl-tRNA synthetase/0.467
1amoFMNNADPH--cytochrome P450 reductase/0.466
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
4psbGA3Cytokinin-specific binding protein/0.465
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.465
1qzyTDEMethionine aminopeptidase 2/0.464
1zgbA1EAcetylcholinesterase3.1.1.70.463
4rxrDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.463
2j3qTFLAcetylcholinesterase3.1.1.70.462
4arbC57Acetylcholinesterase3.1.1.70.462
1qtiGNTAcetylcholinesterase3.1.1.70.461
2oazI96Methionine aminopeptidase 2/0.460
2xujTZ5Acetylcholinesterase3.1.1.70.460
1h22E10Acetylcholinesterase3.1.1.70.459
3qe2FMNNADPH--cytochrome P450 reductase/0.459
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.458
2ea2F77Methionine aminopeptidase 2/0.457
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.457
2ixkTDOdTDP-4-dehydrorhamnose 3,5-epimerase5.1.3.130.456
2xupTZ5Acetylcholinesterase3.1.1.70.456
1zgcA2EAcetylcholinesterase3.1.1.70.455
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.455
2xuhTZ4Acetylcholinesterase3.1.1.70.455
3wqmB29Diterpene synthase3.1.7.80.455
1by5GLY_GLY_GLY_AHO_AHO_AHO_FEFerrichrome-iron receptor/0.454
1r5hAO2Methionine aminopeptidase 2/0.454
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.454
1u65CP0Acetylcholinesterase3.1.1.70.453
2pb1NFGGlucan 1,3-beta-glucosidase/0.453
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.453
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.452
1tllFMNNitric oxide synthase, brain1.14.13.390.451
1yw7A41Methionine aminopeptidase 2/0.451
1zisINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
2gywOBIAcetylcholinesterase3.1.1.70.451
2whqHI6Acetylcholinesterase3.1.1.70.451
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.451
2ea4F79Methionine aminopeptidase 2/0.450
2gv8NDPThiol-specific monooxygenase1.14.130.450
4b7zQ4QAcetylcholinesterase3.1.1.70.450
1ex75GPGuanylate kinase2.7.4.80.449
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.449
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.449
2qimZEAClass 10 plant pathogenesis-related protein/0.449
2xufTZ4Acetylcholinesterase3.1.1.70.449
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4r5wXAVPoly [ADP-ribose] polymerase 12.4.2.300.449
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
1q83TZ5Acetylcholinesterase3.1.1.70.447
2xq0BESLeukotriene A-4 hydrolase homolog3.3.2.60.447
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3mj4URMUDP-galactopyranose mutase/0.447
3t0iSAHPutative methyltransferase/0.447
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.447
1ja1FMNNADPH--cytochrome P450 reductase/0.446
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.446
4ey6GNTAcetylcholinesterase3.1.1.70.446
4wdfA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.446
1gpnHUBAcetylcholinesterase3.1.1.70.445
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.445
3cavCI23-oxo-5-beta-steroid 4-dehydrogenase/0.445
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.445
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3rvhHQ2Lysine-specific demethylase 4A1.14.110.444
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.444
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.444
1icqOPD12-oxophytodienoate reductase 11.3.1.420.443
2ckmAA7Acetylcholinesterase3.1.1.70.443
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.443
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.443
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4jsr1NQNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.443
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.443
3djjFADGlutathione reductase, mitochondrial1.8.1.70.442
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.442
4gd40WSLysine-specific demethylase 4A1.14.110.442
5kwvANPPantothenate synthetase/0.442
1ja0FMNNADPH--cytochrome P450 reductase/0.441
1w76GNTAcetylcholinesterase3.1.1.70.441
1yw9A84Methionine aminopeptidase 2/0.441
2aot2PMHistamine N-methyltransferase2.1.1.80.441
2po3T4K4-dehydrase/0.441
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.441
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.441
4mlp2CXCryptochrome-2/0.441
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.441
1obnASVIsopenicillin N synthase1.21.3.10.440
2g247IGRenin3.4.23.150.440
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.440
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.440
3h3qH13Collagen type IV alpha-3-binding protein/0.440
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.440
4d2dALA_ALA_ALADi-or tripeptide:H+ symporter/0.440