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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
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/1.000
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.513
2v2qNVG4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.509
2bf4FMNNADPH--cytochrome P450 reductase/0.486
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.471
1amoFMNNADPH--cytochrome P450 reductase/0.470
3c1kT15Prothrombin3.4.21.50.469
1ja0FMNNADPH--cytochrome P450 reductase/0.465
2v8pCDP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.464
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.463
1ja1FMNNADPH--cytochrome P450 reductase/0.462
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.459
2v2vV124-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.457
3qe2FMNNADPH--cytochrome P450 reductase/0.457
2gg0U11Methionine aminopeptidase/0.456
1vhzAPRADP compounds hydrolase NudE3.6.10.452
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.449
2bn4FMNNADPH--cytochrome P450 reductase/0.449
4mlp2CXCryptochrome-2/0.448
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.447
2bf4FADNADPH--cytochrome P450 reductase/0.447
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.446
3c49KU8Poly [ADP-ribose] polymerase 32.4.2.300.444
1rfuADPPyridoxal kinase2.7.1.350.443
2gg9U16Methionine aminopeptidase/0.443
2vyqFADFerredoxin--NADP reductase1.18.1.20.442
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.440
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.440
3ojxFMNNADPH--cytochrome P450 reductase/0.440