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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
1akeAP5Adenylate kinase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1akeAP5Adenylate kinase/1.000
2eckADPAdenylate kinase/0.690
4qbiAP5Adenylate kinase/0.615
2osbAP5Adenylate kinase/0.613
1ankANPAdenylate kinase/0.610
4jloADPAdenylate kinase/0.595
3dl0AP5Adenylate kinase/0.584
3hpqAP5Adenylate kinase/0.583
2oo7AP5Adenylate kinase/0.576
4jl5ADPAdenylate kinase/0.571
4qbhAP5Adenylate kinase/0.571
4cf7ADPAdenylate kinase/0.570
4nu0AP5Adenylate kinase/0.569
2qajAP5Adenylate kinase/0.565
4jl6ADPAdenylate kinase/0.564
1e4yAP5Adenylate kinase/0.560
4x8oAP5Adenylate kinase/0.560
1p3jAP5Adenylate kinase/0.558
4w5jAP5Adenylate kinase/0.546
3dkvAP5Adenylate kinase/0.541
4jldADPAdenylate kinase/0.538
3tlxADPAdenylate kinase 2/0.537
4x8lAP5Adenylate kinase/0.524
2akyAP5Adenylate kinase/0.519
4jkyADPAdenylate kinase/0.507
4mkfAP5Adenylate kinase/0.506
2rgxAP5Adenylate kinase/0.504
1oc1ASVIsopenicillin N synthase1.21.3.10.463
2ql6ADPNicotinamide riboside kinase 1/0.463
3zkyWT4Isopenicillin N synthase1.21.3.10.458
2rl1UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.457
5dozNDPJamJ/0.457
2py7ATPPhosphoenolpyruvate carboxykinase (ATP)/0.456
2olrATPPhosphoenolpyruvate carboxykinase (ATP)/0.453
4bb3KKAIsopenicillin N synthase1.21.3.10.453
4ikeADPAdenylate kinase/0.452
3qwfNAP17beta-hydroxysteroid dehydrogenase/0.450
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.449
5k2bZMAAdenosine receptor A2a/0.449
3cisATPUniversal stress protein Rv2623/0.448
3mw9NAIGlutamate dehydrogenase 1, mitochondrial1.4.1.30.448
3s79ASDAromatase1.14.14.140.447
4e07ACPPlasmid partitioning protein ParF/0.447
3cbsR12Cellular retinoic acid-binding protein 2/0.446
3uceNDPDehydrogenase/0.446
2jb4A14Isopenicillin N synthase1.21.3.10.445
2oapANPType II secretion system protein (GspE-2)/0.445
1vl8NAPOxidoreductase, short chain dehydrogenase/reductase family/0.444
2vbpVB1Isopenicillin N synthase1.21.3.10.444
4gllNADUDP-glucuronic acid decarboxylase 14.1.1.350.444
1ju9NADAlcohol dehydrogenase E chain1.1.1.10.443
2iviACWIsopenicillin N synthase1.21.3.10.443
2bu9HFVIsopenicillin N synthase1.21.3.10.442
1qiqACCIsopenicillin N synthase1.21.3.10.441
2vcmM11Isopenicillin N synthase1.21.3.10.441
2wmvZYVSerine/threonine-protein kinase Chk12.7.11.10.441
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.441
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.441
3jynNDPQuinone oxidoreductase/0.440
3mzhCMPCRP-like cAMP-activated global transcriptional regulator/0.440