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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
2plwSAMRibosomal RNA methyltransferase, putative

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2plwSAMRibosomal RNA methyltransferase, putative/1.000
2nyuSAMrRNA methyltransferase 2, mitochondrial/0.549
4n48SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 12.1.1.570.491
5d4uSAMUncharacterized protein MJ0489/0.480
1ydtIQBcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.468
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.468
4y95746Tyrosine-protein kinase/0.467
1pmn984Mitogen-activated protein kinase 102.7.11.240.466
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.466
4kvmSER_ALA_SER_GLU_1XEN-terminal acetyltransferase A complex catalytic subunit ard12.3.1.880.464
4uckSAMLarge structural protein/0.464
5d1nSAHUncharacterized protein/0.464
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.463
4iv8SAMPhosphoethanolamine N-methyltransferase,putative/0.463
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.461
3pb3SAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.459
3w8qAGSDual specificity mitogen-activated protein kinase kinase 12.7.12.20.458
2fznFADBifunctional protein PutA1.5.5.20.457
2p2bPRXAcetyl-coenzyme A synthetase/0.455
3b70NAPEnoyl reductase LovC10.455
1osvCHCBile acid receptor/0.453
4ctkSAMGenome polyprotein/0.453
5ifiPRXAcetyl-coenzyme A synthetase/0.453
4fp9SAM5-methylcytosine rRNA methyltransferase NSUN42.1.10.452
3gqvNAPEnoyl reductase LovC10.451
5e8jSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.451
2y05NAPProstaglandin reductase 1/0.450
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.449
2aa0MTPAdenosine kinase2.7.1.200.448
2uzwSS4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
3sglFADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC/0.448
4fv5EK9Mitogen-activated protein kinase 12.7.11.240.447
1q8tY27cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
2qe6SAMUncharacterized protein/0.446
3rak03ZCyclin-dependent kinase 22.7.11.220.446
1ppjANYCytochrome b/0.445
2xyrSFGReplicase polyprotein 1ab2.1.10.445
3evcSAHGenome polyprotein2.1.1.560.445
3qcx3Q23-phosphoinositide-dependent protein kinase 12.7.11.10.445
3q43D66M1 family aminopeptidase3.4.110.444
4lopSB4Mitogen-activated protein kinase 14/0.444
3nwxKVSGag-Pol polyprotein3.4.23.160.443
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
1gheACOAcetyltransferase2.3.10.442
1kkq471Peroxisome proliferator-activated receptor alpha/0.442
3bg7FADPyranose 2-oxidase/0.442
3fhyATPPyridoxal kinase2.7.1.350.442
3friSAH16S rRNA methylase/0.442
1pg3PRXAcetyl-coenzyme A synthetase/0.441
1w4xFADPhenylacetone monooxygenase1.14.13.920.441
2r3o2SCCyclin-dependent kinase 22.7.11.220.441
3vqsJT1Genome polyprotein/0.441
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.440
4obwSAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial/0.440