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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
1kyv RBF 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1kyv RBF6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 1.132
1kyx CRM6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.888
2a58 RBF6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.868
1ejb INJ6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.849
1kyy INI6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.811
2a59 LMZ6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.811
1nqu RDL6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.800
2a57 CRM6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.795
1nqv LMZ6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.768
1zis INI6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.765
1w29 TS16,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.762
2obx INI6,7-dimethyl-8-ribityllumazine synthase 2 2.5.1.78 0.742
4kq6 DLZ6,7-dimethyl-8-ribityllumazine synthase / 0.739
2nli FMNLactate oxidase / 0.722
1t13 INI6,7-dimethyl-8-ribityllumazine synthase 2 / 0.721
1w19 T5P6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.720
2zfa FMNLactate oxidase / 0.707
4nmc FADBifunctional protein PutA / 0.707
1w19 T1P6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.700
1nqw 5YL6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.696
1siq FADGlutaryl-CoA dehydrogenase, mitochondrial 1.3.8.6 0.694
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.691
3gsi FADDimethylglycine oxidase 1.5.3.10 0.689
3mkh FADNitroalkane oxidase / 0.686
3gdp FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.685
5ebu FMNLactate oxidase / 0.684
2yyi FAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component 1.14.14.9 0.681
1w19 T2P6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.675
2c92 TP66,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.675
2hs6 FMN12-oxophytodienoate reductase 3 1.3.1.42 0.673
3clr FADElectron transfer flavoprotein subunit alpha / 0.673
2pd8 FADVivid PAS protein VVD / 0.669
4opi FDAConserved Archaeal protein / 0.669
4opt FDAConserved Archaeal protein / 0.666
3hjk FADVivid PAS protein VVD / 0.664
5ahs FADAcyl-CoA dehydrogenase / 0.663
3n39 FMNProtein NrdI / 0.662
1kbi FMNCytochrome b2, mitochondrial 1.1.2.3 0.661
2isk FNR5,6-dimethylbenzimidazole synthase 1.13.11.79 0.660
3clt FADElectron transfer flavoprotein subunit alpha / 0.660
3sfe FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.660
1nqx RLP6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.658
1qcw FNSCytochrome b2, mitochondrial 1.1.2.3 0.658
2isj FMN5,6-dimethylbenzimidazole synthase 1.13.11.79 0.658
3nyc FADFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.657
4oxx FMNCindoxin / 0.657
1c0k FADD-amino-acid oxidase 1.4.3.3 0.656
1zrq FAD5,10-methylenetetrahydrofolate reductase 1.5.1.20 0.656
2e48 FADD-amino-acid oxidase 1.4.3.3 0.655
2fja FADAdenylylsulfate reductase, subunit A (AprA) / 0.655
2v1a FMNNPH1-1 / 0.655
1jnr FADAdenylylsulfate reductase, subunit A (AprA) / 0.654
1szf FMNCytochrome b2, mitochondrial 1.1.2.3 0.654
2vxa RBFDodecin / 0.653
2z6d FMNPhototropin-2 2.7.11.1 0.652
4irn FADAnaB / 0.652
4u8m FDAUDP-galactopyranose mutase / 0.652
4u8p FDAUDP-galactopyranose mutase / 0.652
2v0u FMNNPH1-1 / 0.651
2yyl FAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component 1.14.14.9 0.651
3fcj FADNitroalkane oxidase 1.7.3.1 0.651
4opg FDAConserved Archaeal protein / 0.650