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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
3oij SAH Ribosomal RNA small subunit methyltransferase NEP1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3oij SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.942
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.806
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.736
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.722
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.704
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.697
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.693
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.692
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.691
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.691
4x3l MTARNA 2'-O ribose methyltransferase / 0.689
4ib3 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.687
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.683
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.680
4kgn SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.678
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.677
2z08 ATPUniversal stress protein family / 0.676
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
1mjh ATPUniversal stress protein MJ0577 / 0.673
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.673
2qmm SAMtRNA (pseudouridine(54)-N(1))-methyltransferase / 0.672
4btj ATPTau-tubulin kinase 1 2.7.11.1 0.672
2zbv ADNUncharacterized protein / 0.671
4crs AGSSerine/threonine-protein kinase N2 2.7.11.13 0.671
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.671
2ydo ADNAdenosine receptor A2a / 0.670
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.670
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.669
2cx8 SAHRibosomal RNA small subunit methyltransferase E / 0.669
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.669
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.669
3cly ACPFibroblast growth factor receptor 2 / 0.668
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.668
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.668
3bbh SFGRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.666
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.663
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.663
2pml ANPUncharacterized protein / 0.662
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.662
4s1h ADPPyridoxal kinase, putative / 0.662
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.661
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.661
4cnf MTASpoU rRNA methylase / 0.660
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.660
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.659
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.659
3gyq SAM23S rRNA (adenosine(1067)-2'-O)-methyltransferase / 0.659
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.659
2z0y SAMRibosomal RNA small subunit methyltransferase E / 0.658
3hgm ATPTRAP-T-associated universal stress protein TeaD / 0.658
1cm8 ANPMitogen-activated protein kinase 12 / 0.657
4u0o MTALipoyl synthase 2 / 0.657
4xbo SAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ 2.1.1.200 0.657
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.656
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.656
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
2ha8 SAHProbable methyltransferase TARBP1 / 0.654
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.654
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.654
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.654
3fcc ATPD-alanine--poly(phosphoribitol) ligase subunit 1 / 0.653
4bgb ADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases / 0.652
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.650
1kor ANPArgininosuccinate synthase / 0.650
1rfu ADPPyridoxal kinase 2.7.1.35 0.650
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.650