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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
4jwh SAH tRNA (guanine(9)-N1)-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4jwh SAHtRNA (guanine(9)-N1)-methyltransferase / 1.079
4jwf SAHtRNA (guanine(9)-N1)-methyltransferase / 0.896
4jwj SAHtRNA (guanine(9)-N1)-methyltransferase / 0.891
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.727
4cng SAHSpoU rRNA methylase / 0.725
2cx8 SAHRibosomal RNA small subunit methyltransferase E / 0.711
5a7y SAHtRNA (adenine(9)-N1)-methyltransferase 2.1.1.218 0.707
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.706
3bbh SFGRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.693
1uam SAHtRNA (guanine-N(1)-)-methyltransferase 2.1.1.228 0.685
2ha8 SAHProbable methyltransferase TARBP1 / 0.685
4h3y SAHtRNA (guanine-N(1)-)-methyltransferase / 0.683
1mxi SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.682
2z0y SAMRibosomal RNA small subunit methyltransferase E / 0.674
4yvk SFGtRNA (guanine-N(1)-)-methyltransferase 2.1.1.228 0.674
4xbo SAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ 2.1.1.200 0.667
2yy8 MTAtRNA (cytidine(56)-2'-O)-methyltransferase / 0.661
5c1p ADPD-alanine--D-alanine ligase / 0.654
5c1o ANPD-alanine--D-alanine ligase / 0.653
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.651
3rk1 ATPN-type ATP pyrophosphatase superfamily / 0.651