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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
2q93B21Methionine aminopeptidase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2q93B21Methionine aminopeptidase/1.000
2q96A18Methionine aminopeptidase/0.832
2q92B23Methionine aminopeptidase/0.719
2q94A04Methionine aminopeptidase/0.692
2gg2U12Methionine aminopeptidase/0.680
2evmFC2Methionine aminopeptidase/0.675
2evcFC3Methionine aminopeptidase/0.657
3iu7FCDMethionine aminopeptidase 2/0.656
3iu8T03Methionine aminopeptidase 2/0.652
2p98YE7Methionine aminopeptidase/0.650
2p99YE6Methionine aminopeptidase/0.642
2gg8U15Methionine aminopeptidase/0.625
1c23MPHMethionine aminopeptidase/0.609
2gg0U11Methionine aminopeptidase/0.607
2ggbU17Methionine aminopeptidase/0.604
3pkaY02Methionine aminopeptidase 2/0.593
4flkY10Methionine aminopeptidase 1/0.587
2gg3U13Methionine aminopeptidase/0.578
1xnzFCDMethionine aminopeptidase/0.577
2gg9U16Methionine aminopeptidase/0.577
3pkdY10Methionine aminopeptidase 2/0.570
4fliY16Methionine aminopeptidase 1/0.567
3d27W29Methionine aminopeptidase/0.562
4iksTFDMethionine aminopeptidase 1/0.562
2nq7HM5Methionine aminopeptidase 1/0.555
3pkeY10Methionine aminopeptidase 2/0.550
4ikuSHXMethionine aminopeptidase 1/0.549
3pkbY16Methionine aminopeptidase 2/0.545
4fllYZ6Methionine aminopeptidase 1/0.544
4hxx1AYMethionine aminopeptidase 1/0.537
4fljY08Methionine aminopeptidase 1/0.533
4ikrPVPMethionine aminopeptidase 1/0.515
4iktTFVMethionine aminopeptidase 1/0.503
3pkcY08Methionine aminopeptidase 2/0.501
1yw8A75Methionine aminopeptidase 2/0.492
2pb1NFGGlucan 1,3-beta-glucosidase/0.492
2cekN8TAcetylcholinesterase3.1.1.70.488
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.488
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.488
2ea2F77Methionine aminopeptidase 2/0.487
2wzySQXSoluble acetylcholine receptor/0.485
4b7zQ4QAcetylcholinesterase3.1.1.70.484
4zwpM44Xaa-Pro dipeptidase3.4.13.90.484
3zv7NHGAcetylcholinesterase3.1.1.70.482
3wqmB29Diterpene synthase3.1.7.80.480
3g0gRUMDipeptidyl peptidase 4/0.479
1r5hAO2Methionine aminopeptidase 2/0.477
2j3qTFLAcetylcholinesterase3.1.1.70.477
1qzyTDEMethionine aminopeptidase 2/0.476
1w6rGNTAcetylcholinesterase3.1.1.70.476
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.475
2ga2A19Methionine aminopeptidase 2/0.472
2gywOBIAcetylcholinesterase3.1.1.70.472
2ha6SCKAcetylcholinesterase3.1.1.70.472
2xukTZ5Acetylcholinesterase3.1.1.70.472
3mo0SAHHistone-lysine N-methyltransferase EHMT1/0.472
4ey6GNTAcetylcholinesterase3.1.1.70.472
1q84TZ4Acetylcholinesterase3.1.1.70.471
3aezGDPPantothenate kinase2.7.1.330.471
4m0f1YKAcetylcholinesterase3.1.1.70.470
2xufTZ4Acetylcholinesterase3.1.1.70.469
3t0iSAHPutative methyltransferase/0.469
4arbC57Acetylcholinesterase3.1.1.70.469
2xi4AFTAcetylcholinesterase3.1.1.70.468
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.468
1r5gAO1Methionine aminopeptidase 2/0.467
1w4lGL8Acetylcholinesterase3.1.1.70.466
3fktSIIBeta-secretase 13.4.23.460.466
2gyuHI6Acetylcholinesterase3.1.1.70.465
1eveE20Acetylcholinesterase3.1.1.70.464
1lc3NADBiliverdin reductase A1.3.1.240.464
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.464
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.464
3junAKDPhenazine biosynthesis protein A/B/0.464
1x1aSAMC-20 methyltransferase/0.463
2wvlGDDMannosyl-3-phosphogylcerate synthase/0.463
3fhyATPPyridoxal kinase2.7.1.350.463
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.462
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.462
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.462
1w6jR71Lanosterol synthase5.4.99.70.461
3h7rNAPAldo-keto reductase family 4 member C8/0.461
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.460
2xuqTZ4Acetylcholinesterase3.1.1.70.460
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.459
2zsbADPPantothenate kinase2.7.1.330.459
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.459
1yw9A84Methionine aminopeptidase 2/0.458
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.458
2jl1NAPTriphenylmethane reductase/0.458
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.458
3f8sPF2Dipeptidyl peptidase 4/0.458
3lzwNAPFerredoxin--NADP reductase 21.18.1.20.458
1zgbA1EAcetylcholinesterase3.1.1.70.457
2b58COADiamine acetyltransferase 1/0.457
2w6cBM4Acetylcholinesterase3.1.1.70.457
3dz6M8ES-adenosylmethionine decarboxylase proenzyme4.1.1.500.457
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.457
1ni12C5Protein farnesyltransferase subunit beta2.5.1.580.456
1vkgCRIHistone deacetylase 83.5.1.980.456
2xuiTZ5Acetylcholinesterase3.1.1.70.456
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.456
4gd40WSLysine-specific demethylase 4A1.14.110.456
4jtqNAPAldo-keto reductase family 1 member C2/0.456
1r58AO5Methionine aminopeptidase 2/0.455
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.455
2g1s4IGRenin3.4.23.150.455
2ixkTDOdTDP-4-dehydrorhamnose 3,5-epimerase5.1.3.130.455
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.455
3tdvGDPGentamicin resistance protein/0.455
1q45FMN12-oxophytodienoate reductase 31.3.1.420.454
2ed4NAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.454
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.454
2jf0HBPAcetylcholinesterase3.1.1.70.454
2whqHI6Acetylcholinesterase3.1.1.70.454
2xupTZ5Acetylcholinesterase3.1.1.70.454
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.454
1e66HUXAcetylcholinesterase3.1.1.70.453
1fkgSB3Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.453
2aotSAHHistamine N-methyltransferase2.1.1.80.453
3af3GCPPantothenate kinase2.7.1.330.453
3mjrAC2Deoxycytidine kinase2.7.1.740.453
4i101BSBeta-secretase 13.4.23.460.453
4lm4JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
4psbGA3Cytokinin-specific binding protein/0.453
1odcA8BAcetylcholinesterase3.1.1.70.452
2ea4F79Methionine aminopeptidase 2/0.452
3hgoFMN12-oxophytodienoate reductase 31.3.1.420.452
4araC56Acetylcholinesterase3.1.1.70.452
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
4j0t6T9Beta-secretase 13.4.23.460.452
1gky5GPGuanylate kinase2.7.4.80.451
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.451
2aot2PMHistamine N-methyltransferase2.1.1.80.451
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
2xugTZ4Acetylcholinesterase3.1.1.70.451
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3n14FMNXenobiotic reductase/0.451
3nh8DC2N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming)3.5.1.1140.451
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
3ufl508Beta-secretase 13.4.23.460.451
4fsl0VBBeta-secretase 13.4.23.460.451
1dx6GNTAcetylcholinesterase3.1.1.70.450
1ry8RUTAldo-keto reductase family 1 member C3/0.450
1x1bSAHC-20 methyltransferase/0.450
1yw7A41Methionine aminopeptidase 2/0.450
2iyaZIOOleandomycin glycosyltransferase/0.450
2ovyPFJcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.450
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.450
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.450
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.450
4nv10FXFormyl transferase/0.450
1ex75GPGuanylate kinase2.7.4.80.449
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.449
2g247IGRenin3.4.23.150.449
2g6pHM2Methionine aminopeptidase 1/0.449
2xuhTZ4Acetylcholinesterase3.1.1.70.449
2xuoTZ4Acetylcholinesterase3.1.1.70.449
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.449
3ziuLSSLeucyl-tRNA synthetase/0.449
4relKMPGlycosyltransferase/0.449
1qtiGNTAcetylcholinesterase3.1.1.70.448
2getCOKPantothenate kinase2.7.1.330.448
2geuCOKPantothenate kinase2.7.1.330.448
2xujTZ5Acetylcholinesterase3.1.1.70.448
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3h3qH13Collagen type IV alpha-3-binding protein/0.448
3ntrNADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.448
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.448
1gm9SOXPenicillin G acylase3.5.1.110.447
1u65CP0Acetylcholinesterase3.1.1.70.447
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
1zgcA2EAcetylcholinesterase3.1.1.70.447
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.447
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4l0oPLPCystathionine gamma-synthase2.5.1.480.447
4ycpFMNtRNA-dihydrouridine(16) synthase/0.447
1u1gBBBUridine phosphorylase2.4.2.30.446
2c20NADUDP-glucose 4-epimerase/0.446
2qimZEAClass 10 plant pathogenesis-related protein/0.446
2vbqBSJAminoglycoside N(6')-acetyltransferase type 1/0.446
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.446
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.446
4ey7E20Acetylcholinesterase3.1.1.70.446
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3n19FNRXenobiotic reductase/0.445
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.445
4fcd0T6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.445
4m0cFMNFMN-dependent NADH-azoreductase 1/0.445
1ro6ROLcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.444
2oazI96Methionine aminopeptidase 2/0.444
2ovvPFHcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
2zcvNDPQuinone oxidoreductase 21.6.5.20.444
3sxjSAMPutative methyltransferase/0.444
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.444
4mr72BVGamma-aminobutyric acid type B receptor subunit 1/0.444
4yaw2AMNADPH--cytochrome P450 reductase/0.444
1m9hNAD2,5-diketo-D-gluconic acid reductase A1.1.1.3460.443
1rkwPNTHTH-type transcriptional regulator QacR/0.443
1ut6A8NAcetylcholinesterase3.1.1.70.443
1vfsDCSAlanine racemase/0.443
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.443
3g0bT22Dipeptidyl peptidase 4/0.443
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
3kmxG00Beta-secretase 13.4.23.460.443
3rsv3RSBeta-secretase 13.4.23.460.443
3v0p4GWHisto-blood group ABO system transferase/0.443
4bfzZVZPantothenate kinase2.7.1.330.443
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.443
1zw9H64ATP-dependent molecular chaperone HSP82/0.442
2ab8MTPAdenosine kinase2.7.1.200.442
2hs6FMN12-oxophytodienoate reductase 31.3.1.420.442
2uzuL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
3br3ETHTH-type transcriptional regulator QacR/0.442
3ccbB2YDipeptidyl peptidase 4/0.442
3gf4UPGUDP-galactopyranose mutase5.4.99.90.442
3gn73GNPoly [ADP-ribose] polymerase 12.4.2.300.442
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.442
3rthRTHBeta-secretase 13.4.23.460.442
4nv14TGFormyl transferase/0.442
4ts7ADPPurine phosphoribosyltransferase (GpT-1)/0.442
4u140HKMuscarinic acetylcholine receptor M3/0.442
1h66RH1NAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.441
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1x1cSAHC-20 methyltransferase/0.441
2wwjY28Lysine-specific demethylase 4A/0.441
3d91REMRenin3.4.23.150.441
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.441
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
4g8jTHMUridine phosphorylase/0.441
4uthFMNXenobiotic reductase/0.441
2vd7PD2Lysine-specific demethylase 4A1.14.110.440
2zsaADPPantothenate kinase2.7.1.330.440
3fsjD7KBenzoylformate decarboxylase4.1.1.70.440
3h0bB35Beta-secretase 13.4.23.460.440
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.440
3junAJDPhenazine biosynthesis protein A/B/0.440
3juqAJDPhenazine biosynthesis protein A/B/0.440
3qj0QI3Botulinum neurotoxin type A3.4.24.690.440
3vjlW94Dipeptidyl peptidase 4/0.440
4ia05BBcGMP-specific 3',5'-cyclic phosphodiesterase/0.440
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440