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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
1xnzFCDMethionine aminopeptidase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1xnzFCDMethionine aminopeptidase/1.000
2evmFC2Methionine aminopeptidase/0.767
2evcFC3Methionine aminopeptidase/0.752
2q94A04Methionine aminopeptidase/0.728
2q92B23Methionine aminopeptidase/0.714
2p98YE7Methionine aminopeptidase/0.701
2gg2U12Methionine aminopeptidase/0.653
3iu7FCDMethionine aminopeptidase 2/0.641
2q93B21Methionine aminopeptidase/0.626
2p99YE6Methionine aminopeptidase/0.625
3d27W29Methionine aminopeptidase/0.615
2q96A18Methionine aminopeptidase/0.605
3pkeY10Methionine aminopeptidase 2/0.604
2ggbU17Methionine aminopeptidase/0.595
2gg3U13Methionine aminopeptidase/0.589
2gg8U15Methionine aminopeptidase/0.587
2gg9U16Methionine aminopeptidase/0.587
3iu8T03Methionine aminopeptidase 2/0.584
2gg0U11Methionine aminopeptidase/0.578
4ikuSHXMethionine aminopeptidase 1/0.568
4iktTFVMethionine aminopeptidase 1/0.557
1eveE20Acetylcholinesterase3.1.1.70.552
3pkbY16Methionine aminopeptidase 2/0.550
4iksTFDMethionine aminopeptidase 1/0.545
2g6pHM2Methionine aminopeptidase 1/0.544
4fllYZ6Methionine aminopeptidase 1/0.544
1c23MPHMethionine aminopeptidase/0.542
4fliY16Methionine aminopeptidase 1/0.539
1yw8A75Methionine aminopeptidase 2/0.538
2oazI96Methionine aminopeptidase 2/0.538
4hxx1AYMethionine aminopeptidase 1/0.533
1r58AO5Methionine aminopeptidase 2/0.532
3pkcY08Methionine aminopeptidase 2/0.532
4flkY10Methionine aminopeptidase 1/0.526
1dx6GNTAcetylcholinesterase3.1.1.70.525
1r5gAO1Methionine aminopeptidase 2/0.523
2j3qTFLAcetylcholinesterase3.1.1.70.520
2w6cBM4Acetylcholinesterase3.1.1.70.520
3pkaY02Methionine aminopeptidase 2/0.520
2ga2A19Methionine aminopeptidase 2/0.518
1zgbA1EAcetylcholinesterase3.1.1.70.516
2ea2F77Methionine aminopeptidase 2/0.516
4ey7E20Acetylcholinesterase3.1.1.70.514
1h22E10Acetylcholinesterase3.1.1.70.512
3pkdY10Methionine aminopeptidase 2/0.507
4ikrPVPMethionine aminopeptidase 1/0.507
2xufTZ4Acetylcholinesterase3.1.1.70.506
2xuoTZ4Acetylcholinesterase3.1.1.70.506
1r5hAO2Methionine aminopeptidase 2/0.505
2nq7HM5Methionine aminopeptidase 1/0.503
2gywOBIAcetylcholinesterase3.1.1.70.502
4fljY08Methionine aminopeptidase 1/0.502
2jf0HBPAcetylcholinesterase3.1.1.70.499
2xuhTZ4Acetylcholinesterase3.1.1.70.499
2whqHI6Acetylcholinesterase3.1.1.70.498
1u65CP0Acetylcholinesterase3.1.1.70.497
1w4lGL8Acetylcholinesterase3.1.1.70.497
1yw9A84Methionine aminopeptidase 2/0.497
2ea4F79Methionine aminopeptidase 2/0.494
3iu9T07Methionine aminopeptidase 2/0.494
3zv7NHGAcetylcholinesterase3.1.1.70.493
4b7zQ4QAcetylcholinesterase3.1.1.70.493
2xugTZ4Acetylcholinesterase3.1.1.70.492
4araC56Acetylcholinesterase3.1.1.70.492
1qzyTDEMethionine aminopeptidase 2/0.491
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.491
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.490
1yw7A41Methionine aminopeptidase 2/0.489
4ey6GNTAcetylcholinesterase3.1.1.70.489
1odcA8BAcetylcholinesterase3.1.1.70.487
2xukTZ5Acetylcholinesterase3.1.1.70.486
1w6rGNTAcetylcholinesterase3.1.1.70.484
3tdvGDPGentamicin resistance protein/0.482
4gd40WSLysine-specific demethylase 4A1.14.110.482
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.481
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.481
4m0f1YKAcetylcholinesterase3.1.1.70.481
2xuiTZ5Acetylcholinesterase3.1.1.70.480
1gpnHUBAcetylcholinesterase3.1.1.70.475
4arbC57Acetylcholinesterase3.1.1.70.475
2ovvPFHcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.474
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.474
1fkgSB3Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.473
2fm0M98cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.473
2gmsP0PPutative pyridoxamine 5-phosphate-dependent dehydrase/0.473
3qpoPFRcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.472
1q84TZ4Acetylcholinesterase3.1.1.70.471
1y1rANUUridine phosphorylase2.4.2.30.471
1zgcA2EAcetylcholinesterase3.1.1.70.471
4lm4JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.471
1qtiGNTAcetylcholinesterase3.1.1.70.470
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.470
4lcw1VYMajor histocompatibility complex class I-related gene protein/0.470
1by5GLY_GLY_GLY_AHO_AHO_AHO_FEFerrichrome-iron receptor/0.469
2xujTZ5Acetylcholinesterase3.1.1.70.469
2xuqTZ4Acetylcholinesterase3.1.1.70.469
4zwpM44Xaa-Pro dipeptidase3.4.13.90.469
1votHUPAcetylcholinesterase3.1.1.70.467
2ab8MTPAdenosine kinase2.7.1.200.467
2wzySQXSoluble acetylcholine receptor/0.466
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.466
1e6zNGOChitinase/0.465
2fjm073Tyrosine-protein phosphatase non-receptor type 13.1.3.480.465
3f8sPF2Dipeptidyl peptidase 4/0.465
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.465
2pb1NFGGlucan 1,3-beta-glucosidase/0.464
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.464
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.463
2cekN8TAcetylcholinesterase3.1.1.70.463
3mjrAC2Deoxycytidine kinase2.7.1.740.463
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.463
1e2lTMCThymidine kinase/0.462
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.462
3pdqKC6Lysine-specific demethylase 4A1.14.110.462
4ajgF07cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.462
2ckmAA7Acetylcholinesterase3.1.1.70.461
2dg4RAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.461
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.461
4bfxZVXPantothenate kinase2.7.1.330.461
2ha6SCKAcetylcholinesterase3.1.1.70.460
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.460
3zj6VM2Raucaffricine-O-beta-D-glucosidase3.2.1.1250.460
1e66HUXAcetylcholinesterase3.1.1.70.459
1gw2FERPeroxidase C1A1.11.1.70.459
3o5rFK5Peptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.459
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.459
4klaCHDFerrochelatase, mitochondrial4.99.1.10.459
5a4vQUEGlutathione S-transferase F22.5.1.180.459
1q83TZ5Acetylcholinesterase3.1.1.70.458
2xupTZ5Acetylcholinesterase3.1.1.70.458
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
1ex75GPGuanylate kinase2.7.4.80.457
1kw9BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.457
1vkgCRIHistone deacetylase 83.5.1.980.457
2jgbMGTEukaryotic translation initiation factor 4E type 2/0.457
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.457
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.456
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.456
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.456
4q7f3D1Uncharacterized protein/0.456
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.455
1pwyAC2Purine nucleoside phosphorylase2.4.2.10.455
1w6jR71Lanosterol synthase5.4.99.70.455
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.455
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.455
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.455
3qeoLLTDeoxycytidine kinase2.7.1.740.455
3rvhHQ2Lysine-specific demethylase 4A1.14.110.455
4xt8TMQPossible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc/0.455
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.455
1x1bSAHC-20 methyltransferase/0.454
3v0p4GWHisto-blood group ABO system transferase/0.454
1umcTDP2-oxoisovalerate dehydrogenase subunit alpha1.2.4.40.453
1umcTDP2-oxoisovalerate dehydrogenase subunit beta1.2.4.40.453
4cb4MGTPolymerase basic protein 2/0.453
4drn0MCPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.453
4lcnGNGCytidine and deoxycytidylate deaminase zinc-binding region/0.453
4yp6NAPNicotinamide-nucleotide adenylyltransferase2.7.7.10.453
1lgtBP3Biphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.452
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
2gmuPDGPutative pyridoxamine 5-phosphate-dependent dehydrase/0.452
3ccbB2YDipeptidyl peptidase 4/0.452
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.452
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
3zhqTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.452
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.452
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.452
4to2DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.452
1l8qADPChromosomal replication initiator protein DnaA/0.451
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.451
3g0bT22Dipeptidyl peptidase 4/0.451
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.451
4uugPXGBranched-chain amino acid aminotransferase, putative/0.451
5iefNBVNeutral alpha-glucosidase AB3.2.1.840.451
1jwtBLIProthrombin3.4.21.50.450
1rkwPNTHTH-type transcriptional regulator QacR/0.450
2ct8MSPMethionine--tRNA ligase6.1.1.100.450
2gs9SAHUncharacterized protein/0.450
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
3bxoUPPdTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose/0.450
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.450
3lzzGDPUncharacterized protein/0.450
1h60STRPentaerythritol tetranitrate reductase/0.449
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.449
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.449
3wqmB29Diterpene synthase3.1.7.80.449
1oynROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
1tj2FADBifunctional protein PutA1.5.5.20.448
2gyuHI6Acetylcholinesterase3.1.1.70.448
3p67FMNPentaerythritol tetranitrate reductase/0.448
4bftZVTPantothenate kinase2.7.1.330.448
1fkhSBXPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.447
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
4rxrDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.447
1e2nRCAThymidine kinase/0.446
1fkbRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.446
1kw8BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.446
1ro98BRcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.446
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.446
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.446
2xq0BESLeukotriene A-4 hydrolase homolog3.3.2.60.446
2zs8ADPPantothenate kinase2.7.1.330.446
3h3qH13Collagen type IV alpha-3-binding protein/0.446
3qbjNXZDipeptidyl peptidase 4/0.446
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.446
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.446
4psbGA3Cytokinin-specific binding protein/0.446
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.445
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4ld2CTNCytidine and deoxycytidylate deaminase zinc-binding region/0.445
4to4DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.445
1h6aNDPGlucose--fructose oxidoreductase1.1.99.280.444
1kw6BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.444
1ro6ROLcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.444
2ovyPFJcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
2rqfJH3Hemolymph juvenile hormone binding protein/0.444
3b1dPLSBetaC-S lyase/0.444
4to0DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.444
4uthFMNXenobiotic reductase/0.444
1fwyUD1Bifunctional protein GlmU/0.443
1u08PLPMethionine aminotransferase/0.443
2cmfF11Acetylcholinesterase3.1.1.70.443
2iu8UD1UDP-3-O-acylglucosamine N-acyltransferase2.3.10.443
3apwDP0Alpha-1-acid glycoprotein 2/0.443
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.443
1c9hRAPPeptidyl-prolyl cis-trans isomerase FKBP1B5.2.1.80.442
1kwcBPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.442
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.442
2aot2PMHistamine N-methyltransferase2.1.1.80.442
2v19FMNDodecin/0.442
3ab1FADFerredoxin--NADP reductase1.18.1.20.442
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.442
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.442
3rykTYDdTDP-4-dehydrorhamnose 3,5-epimerase/0.442
3sxjSAMPutative methyltransferase/0.442
4drm0MCPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.442
4jt81NRNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.442
4rxqDUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.442
1b2lNDCAlcohol dehydrogenase1.1.1.10.441
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.441
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
2vq7NAPPutative flavin-containing monooxygenase/0.441
3dzkNMNADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.441
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.441
4jfi1KTPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.441
1bx1FADFerredoxin--NADP reductase, chloroplastic1.18.1.20.440
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.440
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.440
2aouCQAHistamine N-methyltransferase2.1.1.80.440
2zevB71Geranylgeranyl pyrophosphate synthase/0.440
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.440
3hxdBD7Geranylgeranyl transferase type-2 subunit beta2.5.1.600.440
3juoAJDPhenazine biosynthesis protein A/B/0.440
3lzwNAPFerredoxin--NADP reductase 21.18.1.20.440
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.440
4a86H35Major pollen allergen Bet v 1-A/0.440
4br0AU1Ectonucleoside triphosphate diphosphohydrolase 2/0.440