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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
1mx0ANPType 2 DNA topoisomerase 6 subunit B

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1mx0ANPType 2 DNA topoisomerase 6 subunit B/1.000
1z5aADPType 2 DNA topoisomerase 6 subunit B/0.606
1z5cADPType 2 DNA topoisomerase 6 subunit B/0.590
2e0aANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.546
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.544
1zxnADPDNA topoisomerase 2-alpha5.99.1.30.531
2zkjADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.519
4r1fADPDNA topoisomerase 2-alpha5.99.1.30.518
3d2rADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.494
1nhhANPDNA mismatch repair protein MutL/0.493
1pvgANPDNA topoisomerase 25.99.1.30.486
1y4sADPChaperone protein HtpG/0.481
1gjvAGS[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial2.7.11.40.480
1thnADPAnti-sigma F factor/0.478
2zdyADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.477
2anb5GPGuanylate kinase2.7.4.80.476
4ipeANPTNF receptor-associated protein 1/0.466
1l0oADPAnti-sigma F factor/0.463
1tilATPAnti-sigma F factor/0.462
3upkUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.460
3i0aDBHNeutrophil gelatinase-associated lipocalin/0.454
2yvwEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.452
2bxoOPBSerum albumin/0.450
4l7j1W2Beta-secretase 13.4.23.460.450
1i59ANPChemotaxis protein CheA2.7.13.30.449
4gt8ADPSensor protein VraS2.7.13.30.448
1i5aACPChemotaxis protein CheA2.7.13.30.447
1u1f183Uridine phosphorylase2.4.2.30.447
3vv8B02Beta-secretase 13.4.23.460.447
1gtrATPGlutamine--tRNA ligase6.1.1.180.446
3zkyWT4Isopenicillin N synthase1.21.3.10.446
1qjfACSIsopenicillin N synthase1.21.3.10.444
3swqEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.444
4bixADPSensor histidine kinase CpxA/0.444
1i5bANPChemotaxis protein CheA2.7.13.30.443
3a0tADPSensor histidine kinase/0.443
3ddw055Glycogen phosphorylase, liver form2.4.1.10.443
3aezGDPPantothenate kinase2.7.1.330.442
4prxADPDNA gyrase subunit B/0.441
1bwlFMNNADPH dehydrogenase 11.6.99.10.440
1qrsATPGlutamine--tRNA ligase6.1.1.180.440
3issEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.440