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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
1qaqSFGrRNA adenine N-6-methyltransferase2.1.1.184

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1qaqSFGrRNA adenine N-6-methyltransferase2.1.1.1841.000
1qanSAHrRNA adenine N-6-methyltransferase2.1.1.1840.596
1qaoSAMrRNA adenine N-6-methyltransferase2.1.1.1840.592
3grrSAHProbable ribosomal RNA small subunit methyltransferase A/0.521
2nyuSAMrRNA methyltransferase 2, mitochondrial/0.502
4mwzSAMPhosphoethanolamine N-methyltransferase, putative/0.497
5bxySAHPutative RNA methylase family UPF0020/0.491
2plwSAMRibosomal RNA methyltransferase, putative/0.485
3q87SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY)/0.484
2i9kSAHModification methylase HhaI2.1.1.370.482
4gc9SAMDimethyladenosine transferase 1, mitochondrial2.1.10.479
1nv8SAMRelease factor glutamine methyltransferase2.1.1.2970.476
3ckxSTUSerine/threonine-protein kinase 242.7.11.10.475
4fr0SAMArsenic methyltransferase/0.475
3uj8SFGPhosphoethanolamine N-methyltransferase/0.473
5bw4SAMUncharacterized protein/0.472
2h3wCOACarnitine O-acetyltransferase2.3.1.70.470
4iv0SAMPhosphoethanolamine N-methyltransferase, putative/0.469
5epeSAHUncharacterized protein/0.469
1lsoNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.468
4loqSB4Mitogen-activated protein kinase 14/0.467
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.466
3qzfX66Cyclin-dependent kinase 22.7.11.220.465
1kkq471Peroxisome proliferator-activated receptor alpha/0.464
1ve3SAMUncharacterized protein/0.460
3uj7SAMPhosphoethanolamine N-methyltransferase/0.460
4g6hNAIRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.460
4qmpDKISerine/threonine-protein kinase 242.7.11.10.460
2xikJ60Serine/threonine-protein kinase 252.7.11.10.459
2vwpNDPGlucose 1-dehydrogenase/0.458
3hdmMMGSerine/threonine-protein kinase Sgk12.7.11.10.458
4ri1ACOUDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase2.3.1.2020.458
4lxhC1EAlpha/beta hydrolase fold/0.457
3ha5SFGHydroxymycolate synthase MmaA42.1.10.456
3qxoX65Cyclin-dependent kinase 22.7.11.220.456
3rmf20ZCyclin-dependent kinase 22.7.11.220.456
3zsi52PMitogen-activated protein kinase 14/0.456
4fgzSAHPhosphoethanolamine N-methyltransferase/0.456
1xddAAYIntegrin alpha-L/0.455
2a1nCAMCamphor 5-monooxygenase1.14.15.10.455
3pb3SAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.455
4lopSB4Mitogen-activated protein kinase 14/0.455
2z54AB1Gag-Pol polyprotein3.4.23.160.454
3wblPDYCyclin-dependent kinase 22.7.11.220.454
4g73NAIRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.454
1q8uH52cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.453
3tljSAHUncharacterized protein/0.453
4bznUGXSerine/threonine-protein kinase pim-12.7.11.10.453
4l8u9AZSerum albumin/0.453
1kf6FADFumarate reductase flavoprotein subunit1.3.5.40.452
2qe6SAMUncharacterized protein/0.452
2vtjLZ4Cyclin-dependent kinase 22.7.11.220.452
2ww4ADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.452
3t2zFADSulfide-quinone reductase/0.452
3evcSAHGenome polyprotein2.1.1.560.451
3l9nL9NcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
1orrNADCDP-paratose 2-epimerase/0.450
2gtnLIEMitogen-activated protein kinase 14/0.450
2w06FRVCyclin-dependent kinase 22.7.11.220.450
2z6uSAHModification methylase HhaI2.1.1.370.450
3a7jADPSerine/threonine-protein kinase 242.7.11.10.450
3fpjSAMUncharacterized protein/0.450
3v9v21LPeroxisome proliferator-activated receptor gamma/0.450
1kfbIGPTryptophan synthase alpha chain/0.449
1kzjCB3Thymidylate synthase/0.449
2oc4IMHPurine nucleoside phosphorylase2.4.2.10.449
3busSAHDemethylrebeccamycin-D-glucose O-methyltransferase/0.449
3p9kSAHCaffeic acid O-methyltransferase/0.449
3ral04ZCyclin-dependent kinase 22.7.11.220.449
3sr4TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific2.1.1.430.449
1bygSTUTyrosine-protein kinase CSK/0.448
1w4xFADPhenylacetone monooxygenase1.14.13.920.448
2he5NDPAldo-keto reductase family 1 member C211.1.10.448
2q29ACOOxalyl-CoA decarboxylase4.1.1.80.448
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.448
3t3r9PLCytochrome P450 2A61.14.130.448
4eudCOASuccinyl-CoA:acetate CoA-transferase/0.448
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.448
1drhNAPDihydrofolate reductase1.5.1.30.447
1ju9NADAlcohol dehydrogenase E chain1.1.1.10.447
1sg9SAMRelease factor glutamine methyltransferase2.1.1.2970.447
1t85CAMCamphor 5-monooxygenase1.14.15.10.447
1zemNADXylitol dehydrogenase/0.447
2np7NEAModification methylase TaqI2.1.1.720.447
2vttLZDCyclin-dependent kinase 22.7.11.220.447
3bbtFMMReceptor tyrosine-protein kinase erbB-42.7.10.10.447
3qd33Q53-phosphoinositide-dependent protein kinase 12.7.11.10.447
1jmhUMPThymidylate synthase/0.446
2b5vNAPGlucose 1-dehydrogenase/0.446
2c6tDT5Cyclin-dependent kinase 22.7.11.220.446
2ibtNEAModification methylase TaqI2.1.1.720.446
2r3kSCQCyclin-dependent kinase 22.7.11.220.446
3h8bNSYCathepsin L13.4.22.150.446
3p2kSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.446
3pj8404Cyclin-dependent kinase 22.7.11.220.446
4eueNAITrans-2-enoyl-CoA reductase [NADH]/0.446
4q72FADBifunctional protein PutA/0.446
1dm2HMDCyclin-dependent kinase 22.7.11.220.445
1owoFADDeoxyribodipyrimidine photo-lyase4.1.99.30.445
1xp6AIUEstrogen receptor/0.445
2aouCQAHistamine N-methyltransferase2.1.1.80.445
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.445
3rk708ZCyclin-dependent kinase 22.7.11.220.445
3te4ACODopamine N-acetyltransferase/0.445
4nmdFDABifunctional protein PutA/0.445
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1t88CAMCamphor 5-monooxygenase1.14.15.10.444
1tj1FADBifunctional protein PutA1.5.5.20.444
2ih2NEAModification methylase TaqI2.1.1.720.444
2ijgFADCryptochrome DASH, chloroplastic/mitochondrial/0.444
2vo7M05cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.444
3qtqX35Cyclin-dependent kinase 22.7.11.220.444
4q71FADBifunctional protein PutA/0.444
4qmlANPSerine/threonine-protein kinase 242.7.11.10.444
5d1nSAHUncharacterized protein/0.444
2ociTYCValacyclovir hydrolase3.10.443
3swrSFGDNA (cytosine-5)-methyltransferase 12.1.1.370.443
3tm5SFGUncharacterized protein/0.443
4ek9EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific2.1.1.430.443
1owmFADDeoxyribodipyrimidine photo-lyase4.1.99.30.442
2hw2RFPRifampin ADP-ribosyl transferase/0.442
2vthLZ2Cyclin-dependent kinase 22.7.11.220.442
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.442
6cp4CAMCamphor 5-monooxygenase1.14.15.10.442
1gih1PUCyclin-dependent kinase 22.7.11.220.441
1tllFADNitric oxide synthase, brain1.14.13.390.441
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.441
3iaeD7KBenzaldehyde lyase/0.441
4a8v2ANMajor pollen allergen Bet v 1-J/0.441
4obwSAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial/0.441
4r6xSAHPhosphoethanolamine N-methyltransferase/0.441
1dhiMTXDihydrofolate reductase1.5.1.30.440
1f123HCHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.440
1osvCHCBile acid receptor/0.440
1qoqIGPTryptophan synthase alpha chain/0.440
1ydrIQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
2cibCM6Lanosterol 14-alpha demethylase1.14.13.700.440
2gjlFMNNitronate monooxygenase1.13.12.160.440
2w3bNDPDihydrofolate reductase1.5.1.30.440
2x7gPVBSRSF protein kinase 22.7.11.10.440
3a7hATPSerine/threonine-protein kinase 242.7.11.10.440
3r8zZ63Cyclin-dependent kinase 22.7.11.220.440
3sw719KCyclin-dependent kinase 22.7.11.220.440
4e4m0NHTyrosine-protein kinase JAK2/0.440
4eji0QACytochrome P450 2A131.14.14.10.440
4oplFDAConserved Archaeal protein/0.440
5e5h0T1Succinyl-CoA:acetate CoA-transferase/0.440
2ycxP32Beta-1 adrenergic receptor/0.440