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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
3o7b SAH Ribosomal RNA small subunit methyltransferase Nep1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.941
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.753
2cx8 SAHRibosomal RNA small subunit methyltransferase E / 0.746
2qmm SAMtRNA (pseudouridine(54)-N(1))-methyltransferase / 0.746
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.738
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.730
4jwh SAHtRNA (guanine(9)-N1)-methyltransferase / 0.727
5a7y SAHtRNA (adenine(9)-N1)-methyltransferase 2.1.1.218 0.723
3oij SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.722
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.718
3bbh SFGRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.699
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.697
4jwj SAHtRNA (guanine(9)-N1)-methyltransferase / 0.694
3wnz ADPAlanine--anticapsin ligase / 0.693
5ahw CMPUniversal stress protein family protein, putative / 0.691
4jwf SAHtRNA (guanine(9)-N1)-methyltransferase / 0.686
3rk1 ATPN-type ATP pyrophosphatase superfamily / 0.685
4cng SAHSpoU rRNA methylase / 0.684
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.680
1mjh ATPUniversal stress protein MJ0577 / 0.677
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.677
3hgm ATPTRAP-T-associated universal stress protein TeaD / 0.677
3n4k SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.677
4xfj ANPArgininosuccinate synthase / 0.676
1s16 ANPDNA topoisomerase 4 subunit B / 0.675
4kgn SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.675
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.675
4cnf MTASpoU rRNA methylase / 0.674
4yvh SFGtRNA (guanine-N(1)-)-methyltransferase 2.1.1.228 0.672
2ha8 SAHProbable methyltransferase TARBP1 / 0.671
4x3l MTARNA 2'-O ribose methyltransferase / 0.671
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.667
2e8r SAHDiphthine synthase / 0.665
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.665
1kh2 ATPArgininosuccinate synthase / 0.661
2wsi FADFAD synthase 2.7.7.2 0.661
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.660
4h3z SAHtRNA (guanine-N(1)-)-methyltransferase / 0.660
2p0a ANPSynapsin-3 / 0.659
3gyq SAM23S rRNA (adenosine(1067)-2'-O)-methyltransferase / 0.659
4ffr ATPUncharacterized protein / 0.658
5c1p ADPD-alanine--D-alanine ligase / 0.658
1kor ANPArgininosuccinate synthase / 0.657
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.657
4ffl ADPUncharacterized protein / 0.657
1kp3 ATPArgininosuccinate synthase 6.3.4.5 0.656
2z0y SAMRibosomal RNA small subunit methyltransferase E / 0.656
2ybo SAHMethyltransferase / 0.655
4jlp ADPAdenylate kinase / 0.655
1j1z ATPArgininosuccinate synthase / 0.654
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.654
5c1o ANPD-alanine--D-alanine ligase / 0.654
2aj4 ANPGalactokinase 2.7.1.6 0.652
2ejz SAHDiphthine synthase / 0.652
1v9o ADPSignaling protein / 0.651
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.650
3ndc SAHPrecorrin-4 C(11)-methyltransferase 2.1.1.133 0.650