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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
4ikuSHXMethionine aminopeptidase 1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4ikuSHXMethionine aminopeptidase 1/1.000
4ikrPVPMethionine aminopeptidase 1/0.820
4iktTFVMethionine aminopeptidase 1/0.748
4fliY16Methionine aminopeptidase 1/0.727
3pkeY10Methionine aminopeptidase 2/0.658
1c23MPHMethionine aminopeptidase/0.644
2g6pHM2Methionine aminopeptidase 1/0.641
2nq7HM5Methionine aminopeptidase 1/0.637
2gg0U11Methionine aminopeptidase/0.629
2gg8U15Methionine aminopeptidase/0.629
3iu8T03Methionine aminopeptidase 2/0.627
4hxx1AYMethionine aminopeptidase 1/0.627
2evcFC3Methionine aminopeptidase/0.621
3pkdY10Methionine aminopeptidase 2/0.620
4iksTFDMethionine aminopeptidase 1/0.618
2ggbU17Methionine aminopeptidase/0.611
3pkaY02Methionine aminopeptidase 2/0.606
2evmFC2Methionine aminopeptidase/0.604
3iu7FCDMethionine aminopeptidase 2/0.603
4fllYZ6Methionine aminopeptidase 1/0.602
2gg3U13Methionine aminopeptidase/0.592
4flkY10Methionine aminopeptidase 1/0.591
2q92B23Methionine aminopeptidase/0.587
3pkbY16Methionine aminopeptidase 2/0.578
2q93B21Methionine aminopeptidase/0.565
3d27W29Methionine aminopeptidase/0.559
1xnzFCDMethionine aminopeptidase/0.555
2gg9U16Methionine aminopeptidase/0.555
2q94A04Methionine aminopeptidase/0.554
2p99YE6Methionine aminopeptidase/0.553
3pkcY08Methionine aminopeptidase 2/0.553
2gg2U12Methionine aminopeptidase/0.543
2q96A18Methionine aminopeptidase/0.539
3iu9T07Methionine aminopeptidase 2/0.535
2p98YE7Methionine aminopeptidase/0.530
4fljY08Methionine aminopeptidase 1/0.524
2ga2A19Methionine aminopeptidase 2/0.519
1qzyTDEMethionine aminopeptidase 2/0.516
2oazI96Methionine aminopeptidase 2/0.516
1r5gAO1Methionine aminopeptidase 2/0.513
1yw9A84Methionine aminopeptidase 2/0.509
2j3qTFLAcetylcholinesterase3.1.1.70.509
1eveE20Acetylcholinesterase3.1.1.70.507
2ea2F77Methionine aminopeptidase 2/0.505
1zgbA1EAcetylcholinesterase3.1.1.70.503
2w6cBM4Acetylcholinesterase3.1.1.70.496
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.494
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.490
1yw8A75Methionine aminopeptidase 2/0.488
1odcA8BAcetylcholinesterase3.1.1.70.485
5c1mCLRMu-type opioid receptor/0.483
2fs4PZ1Renin3.4.23.150.482
1v08NTZ4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic3.2.1.1820.481
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.480
1amoFMNNADPH--cytochrome P450 reductase/0.479
2ea4F79Methionine aminopeptidase 2/0.479
2xi4AFTAcetylcholinesterase3.1.1.70.477
2gywOBIAcetylcholinesterase3.1.1.70.476
2xugTZ4Acetylcholinesterase3.1.1.70.474
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.474
4m0f1YKAcetylcholinesterase3.1.1.70.474
1r5hAO2Methionine aminopeptidase 2/0.472
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.472
3pdqKC6Lysine-specific demethylase 4A1.14.110.472
4isuIKMGlutamate receptor 2/0.472
2xupTZ5Acetylcholinesterase3.1.1.70.469
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.469
2cekN8TAcetylcholinesterase3.1.1.70.468
3hmvHBTcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.468
1zgcA2EAcetylcholinesterase3.1.1.70.467
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.467
2iyaZIOOleandomycin glycosyltransferase/0.467
3rtnRTNBeta-secretase 13.4.23.460.467
1tllFMNNitric oxide synthase, brain1.14.13.390.465
2aouCQAHistamine N-methyltransferase2.1.1.80.465
2pb1NFGGlucan 1,3-beta-glucosidase/0.465
2ovyPFJcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.464
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.463
1yw7A41Methionine aminopeptidase 2/0.462
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.462
2xuhTZ4Acetylcholinesterase3.1.1.70.462
4q7f3D1Uncharacterized protein/0.461
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.459
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.459
3ufl508Beta-secretase 13.4.23.460.459
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.458
3f90FMNFlavodoxin/0.458
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.458
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.458
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.458
1oynROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.457
2xuqTZ4Acetylcholinesterase3.1.1.70.457
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.457
2g263LGRenin3.4.23.150.456
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.456
3rvhHQ2Lysine-specific demethylase 4A1.14.110.456
3v94WYQPhosphodiesterase/0.456
4arbC57Acetylcholinesterase3.1.1.70.456
4ey6GNTAcetylcholinesterase3.1.1.70.456
4ia05BBcGMP-specific 3',5'-cyclic phosphodiesterase/0.456
4r5wXAVPoly [ADP-ribose] polymerase 12.4.2.300.456
1esmCOAPantothenate kinase2.7.1.330.455
2aovC2MHistamine N-methyltransferase2.1.1.80.455
2jf0HBPAcetylcholinesterase3.1.1.70.455
2xukTZ5Acetylcholinesterase3.1.1.70.455
3owxXRARibosyldihydronicotinamide dehydrogenase [quinone]/0.455
4gd40WSLysine-specific demethylase 4A1.14.110.455
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.454
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.454
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4gtt7TQGeranylgeranyl transferase type-2 subunit beta2.5.1.600.454
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.454
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
2yyeAPCSelenide, water dikinase2.7.9.30.453
3rsv3RSBeta-secretase 13.4.23.460.453
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.452
2wcgMT5Glucosylceramidase3.2.1.450.452
3apwDP0Alpha-1-acid glycoprotein 2/0.452
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.452
1paxDHQPoly [ADP-ribose] polymerase 12.4.2.300.451
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
2ct8MSPMethionine--tRNA ligase6.1.1.100.451
3af3GCPPantothenate kinase2.7.1.330.451
3c3xNAPEugenol synthase 11.1.1.3180.451
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.451
1q84TZ4Acetylcholinesterase3.1.1.70.450
1vkgCRIHistone deacetylase 83.5.1.980.450
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.450
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.449
2xujTZ5Acetylcholinesterase3.1.1.70.449
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.449
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.449
4b7zQ4QAcetylcholinesterase3.1.1.70.449
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.449
4g2yNI5cGMP-specific 3',5'-cyclic phosphodiesterase/0.449
4zwpM44Xaa-Pro dipeptidase3.4.13.90.449
2g274LGRenin3.4.23.150.448
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.447
2g1y5IGRenin3.4.23.150.447
3caqNDP3-oxo-5-beta-steroid 4-dehydrogenase/0.447
3i0oSMISpectinomycin phosphotransferase/0.447
3lutNAPVoltage-gated potassium channel subunit beta-2/0.447
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.447
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
1r58AO5Methionine aminopeptidase 2/0.446
1w6rGNTAcetylcholinesterase3.1.1.70.446
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.446
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.446
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
3s8pSAMHistone-lysine N-methyltransferase KMT5B2.1.1.430.445
4drhRAPSerine/threonine-protein kinase mTOR2.7.11.10.445
4drhRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.445
4ey7E20Acetylcholinesterase3.1.1.70.445
5a4vQUEGlutathione S-transferase F22.5.1.180.445
2oz57XYUncharacterized protein/0.444
2xweAMFGlucosylceramidase3.2.1.450.444
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.444
3g72A6TRenin3.4.23.150.444
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.444
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.444
1obnASVIsopenicillin N synthase1.21.3.10.443
2wm3NFLNmrA-like family domain-containing protein 1/0.443
2wzySQXSoluble acetylcholine receptor/0.443
3b6pTMPThree-prime repair exonuclease 13.1.11.20.443
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.443
3wqmB29Diterpene synthase3.1.7.80.443
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.443
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.443
4jq4IMNAldo-keto reductase family 1 member C2/0.443
3d4sTIMBeta-2 adrenergic receptor/0.443
3nyaJTZBeta-2 adrenergic receptor/0.443
1ex75GPGuanylate kinase2.7.4.80.442
2cdaNAPGlucose 1-dehydrogenase/0.442
2fm0M98cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
2zsbADPPantothenate kinase2.7.1.330.442
3bjcWANcGMP-specific 3',5'-cyclic phosphodiesterase/0.442
3djjFADGlutathione reductase, mitochondrial1.8.1.70.442
3h7rNAPAldo-keto reductase family 4 member C8/0.442
4qoeFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.442
5ah5LSSLeucine--tRNA ligase/0.442
1jf0CZHObelin/0.441
3ox1695Ribosyldihydronicotinamide dehydrogenase [quinone]/0.441
3v0m5GWHisto-blood group ABO system transferase/0.441
1mxfMTXPutative pteridine reductase 2/0.440
2bf4FADNADPH--cytochrome P450 reductase/0.440
2qimZEAClass 10 plant pathogenesis-related protein/0.440
2xq0BESLeukotriene A-4 hydrolase homolog3.3.2.60.440
3myuVIBHigh affinity transport system protein p37/0.440
4zvnFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.440