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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
3b03 VNR Isopentenyl-diphosphate delta-isomerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3b03 VNRIsopentenyl-diphosphate delta-isomerase / 1.692
2zry FNRIsopentenyl-diphosphate delta-isomerase / 1.316
3b05 FNRIsopentenyl-diphosphate delta-isomerase / 1.302
2zru FMNIsopentenyl-diphosphate delta-isomerase / 1.290
2zrv FNRIsopentenyl-diphosphate delta-isomerase / 1.278
2zrz FNRIsopentenyl-diphosphate delta-isomerase / 1.264
3b04 OOPIsopentenyl-diphosphate delta-isomerase / 1.254
2zrx FMNIsopentenyl-diphosphate delta-isomerase / 1.210
3vkj FNRIsopentenyl-diphosphate delta-isomerase / 1.196
4qnw FMNChanoclavine-I aldehyde reductase easA / 0.801
3l67 FMNXenobiotic reductase / 0.758
2abb FMNPentaerythritol tetranitrate reductase / 0.742
4utk FNRXenobiotic reductase / 0.742
1q45 FMN12-oxophytodienoate reductase 3 1.3.1.42 0.735
1szf FMNCytochrome b2, mitochondrial 1.1.2.3 0.731
4e2b FMNDehydrogenase / 0.725
1oya FMNNADPH dehydrogenase 1 1.6.99.1 0.720
2h8x FMNXenA / 0.720
1kbq FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.714
1icq FMN12-oxophytodienoate reductase 1 1.3.1.42 0.705
1h63 FMNPentaerythritol tetranitrate reductase / 0.698
1kbo FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.694
3atz FMNProstaglandin F2a synthase / 0.694
1d4a FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.693
3p74 FMNPentaerythritol tetranitrate reductase / 0.693
4rnv FMNNADPH dehydrogenase 1 1.6.99.1 0.687
1qbg FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.680
1gox FMNPeroxisomal (S)-2-hydroxy-acid oxidase 1.1.3.15 0.675
2ohh FMNType A flavoprotein FprA 1 0.675
1dxq FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.670
4j8p FMNFlavodoxin / 0.667
3hgr FMN12-oxophytodienoate reductase 1 1.3.1.42 0.665
2z9d FMNFMN-dependent NADH-azoreductase / 0.663
1bwl FMNNADPH dehydrogenase 1 1.6.99.1 0.662
3m0o FADMonomeric sarcosine oxidase 1.5.3.1 0.662
3lnc 5GPGuanylate kinase / 0.660
4yco FMNtRNA-dihydrouridine(16) synthase / 0.659
1yob FMNFlavodoxin 2 / 0.657
2fcr FMNFlavodoxin / 0.657
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.656
2bi8 FADUDP-galactopyranose mutase 5.4.99.9 0.655
1wam FADUDP-galactopyranose mutase 5.4.99.9 0.653