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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3oab DST Geranyl diphosphate synthase large subunit

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3oab DSTGeranyl diphosphate synthase large subunit / 1.048
3krf DSTGeranyl diphosphate synthase large subunit / 0.847
4dwb 0M7Farnesyl pyrophosphate synthase / 0.741
1yv5 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.734
4ga3 4GAFarnesyl pyrophosphate synthase 2.5.1.10 0.713
1rqj RISFarnesyl diphosphate synthase 2.5.1.10 0.707
3n0z 3ATAdenylate cyclase 2 / 0.696
4h5d YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.695
3rye UNRFarnesyl pyrophosphate synthase 2.5.1.10 0.693
1xjj DGTVitamin B12-dependent ribonucleotide reductase / 0.692
3tb9 ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.690
2z4w 749Geranylgeranyl pyrophosphate synthase / 0.689
4h5e YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.689
4dem YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.688
3s87 DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.686
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.685
3zcb ATPAdenosine monophosphate-protein transferase VbhT 2.7.7.n1 0.685
1xjk DGTVitamin B12-dependent ribonucleotide reductase / 0.678
3ryw K9HFarnesyl pyrophosphate synthase, putative / 0.677
4lfv YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.675
4qec NAPElxO / 0.674
2cvu ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.673
4psg NOHThymidylate synthase / 0.670
4l2x YL2Farnesyl pyrophosphate synthase 2.5.1.10 0.669
4bri UNPEctonucleoside triphosphate diphosphohydrolase I / 0.668
2vp0 TTPDeoxynucleoside kinase / 0.667
1oe0 TTPDeoxynucleoside kinase / 0.666
3dk4 NDPGlutathione reductase, mitochondrial 1.8.1.7 0.665
5itz GTPTubulin alpha-1B chain / 0.661
4o4l GTPTubulin alpha-1B chain / 0.659
3v2u ATPProtein GAL3 / 0.658
4u0s ADPAdenosine monophosphate-protein transferase FICD 2.7.7.n1 0.658
2zzc NAPThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.657
3koy Z97D-ornithine 4,5-aminomutase subunit beta / 0.655
3lzw NAPFerredoxin--NADP reductase 2 1.18.1.2 0.655
4l03 NAPIsocitrate dehydrogenase [NADP] cytoplasmic 1.1.1.42 0.655
3l77 NJPShort-chain alcohol dehydrogenase / 0.654
3tn7 NJPShort-chain alcohol dehydrogenase / 0.653
4b4o NDPEpimerase family protein SDR39U1 / 0.653
1peq TTPRibonucleoside-diphosphate reductase 2 subunit alpha 1.17.4.1 0.650
2z52 H23Geranylgeranyl pyrophosphate synthase / 0.650