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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
4yuvS4MSpermidine synthase, putative

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4yuvS4MSpermidine synthase, putative/1.000
4yuzS4MSpermidine synthase, putative/0.607
4yv0S4MSpermidine synthase, putative/0.532
2pt6S4MSpermidine synthase/0.528
3rw9DSHSpermidine synthase2.5.1.160.511
4yv2S4MSpermidine synthase, putative/0.482
1ydtIQBcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.475
2o07MTASpermidine synthase2.5.1.160.475
4axaRKDcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.474
4yv1S4MSpermidine synthase, putative/0.474
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.473
3ow3SMYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.473
1q8uH52cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.471
1q8wM77cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.470
3fwsANPTranscriptional repressor CcpN/0.469
3fwrADPTranscriptional repressor CcpN/0.468
4kb9G79Protease/0.468
2o06MTASpermidine synthase2.5.1.160.465
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.465
1geeNADGlucose 1-dehydrogenase1.1.1.470.464
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.461
2i0dMUTProtease/0.460
3bwcSAMSpermidine synthase, putative/0.460
1ppl1Z7Penicillopepsin-13.4.23.200.459
1i9gSAMtRNA (adenine(58)-N(1))-methyltransferase TrmI/0.457
3lhdSAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI2.1.1.2190.455
3s85LK0Gag-Pol polyprotein/0.455
1xjdSTUProtein kinase C theta type2.7.11.130.454
3ijrNADOxidoreductase, short chain dehydrogenase/reductase family/0.454
1ppkIVVPenicillopepsin-13.4.23.200.453
1kr5SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase2.1.1.770.452
2b53D23Cyclin-dependent kinase 22.7.11.220.452
3lovFADProtoporphyrinogen oxidase/0.452
4ykgFADAlkyl hydroperoxide reductase subunit F1.8.10.452
1d4jMSCGag-Pol polyprotein3.4.23.160.451
2xlrFADPutative flavin-containing monooxygenase/0.451
4a4qUX9Pol protein/0.451
1msmJE2Gag-Pol polyprotein3.4.23.160.450
2vo6M05cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
2wmtZYTSerine/threonine-protein kinase Chk12.7.11.10.450
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.450
1e3sNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.449
1g1aNADdTDP-glucose 4,6-dehydratase/0.449
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
4bidIE8Mitogen-activated protein kinase kinase kinase 52.7.11.250.449
4hnf16WCasein kinase I isoform delta2.7.11.10.449
1nvqUCNSerine/threonine-protein kinase Chk12.7.11.10.448
1w4xFADPhenylacetone monooxygenase1.14.13.920.448
2ylzFADPhenylacetone monooxygenase1.14.13.920.448
3em3478Gag-Pol polyprotein3.4.23.160.448
3lkhLT6Genome polyprotein2.7.7.480.448
3qvpFADGlucose oxidase1.1.3.40.448
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.448
1sveI01cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
2uw6GVOcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
2uzwSS4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
2ym44YMSerine/threonine-protein kinase Chk12.7.11.10.447
3oijSAHRibosomal RNA small subunit methyltransferase NEP1/0.447
4ctkSAMGenome polyprotein/0.447
1rwbNADGlucose 1-dehydrogenase1.1.1.470.446
2i0aMUIProtease/0.446
2j08FADDeoxyribodipyrimidine photo-lyase4.1.99.30.446
3cic316Beta-secretase 13.4.23.460.446
3sacAF8Protease/0.446
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.446
4kvzSAHPtnL protein/0.446
1gesFADGlutathione reductase1.8.1.70.445
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.445
3zo4QWIcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.445
3zpsEQMGag-Pol polyprotein3.4.23.160.445
4d86ADPPoly [ADP-ribose] polymerase 142.4.2.300.445
4opgFDAConserved Archaeal protein/0.445
1t7i017Gag-Pol polyprotein3.4.23.160.444
2wxvWXVCyclin-dependent kinase 22.7.11.220.444
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.444
4idgNADPutative UDP-glucose 4-epimerase/0.444
1hsgMK1Gag-Pol polyprotein/0.443
3d1xROCGag-Pol polyprotein3.4.23.160.443
3sr4TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific2.1.1.430.443
3vyeVYERenin3.4.23.150.443
4rdiATPtRNA threonylcarbamoyladenosine dehydratase6.10.443
5ayzNCNNicotinate-nucleotide pyrophosphorylase [carboxylating]2.4.2.190.443
1m0b0ZQGag-Pol polyprotein3.4.23.160.442
1u3cFADCryptochrome-1/0.442
2uw7GVPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
3lzv017Gag-Pol polyprotein3.4.23.160.442
3qrsNK8Gag-Pol polyprotein3.4.23.160.442
4dfg0JVGag-Pol polyprotein3.4.23.160.442
4jn9FADDepH/0.442
4mv8ACPBiotin carboxylase6.3.4.140.442
1bxoPP7Penicillopepsin-13.4.23.200.441
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.441
3iobA4DPantothenate synthetase6.3.2.10.441
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.441
1lceTMFThymidylate synthase/0.440
1qrpHH0Pepsin A-43.4.23.10.440
2vo0M03cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
3pwm017Gag-Pol polyprotein3.4.23.160.440
4bf2STUMitogen-activated protein kinase kinase kinase 52.7.11.250.440