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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
4pzk SAH Putative tRNA (cytidine(34)-2'-O)-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 1.032
4x3l MTARNA 2'-O ribose methyltransferase / 0.858
4kgn SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.842
4cng SAHSpoU rRNA methylase / 0.836
4cnf MTASpoU rRNA methylase / 0.825
3n4k SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.820
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.791
4jal SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.790
2ha8 SAHProbable methyltransferase TARBP1 / 0.784
4xbo SAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ 2.1.1.200 0.751
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.735
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.732
3gyq SAM23S rRNA (adenosine(1067)-2'-O)-methyltransferase / 0.730
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.730
2z08 ATPUniversal stress protein family / 0.721
1kp3 ATPArgininosuccinate synthase 6.3.4.5 0.718
1kor ANPArgininosuccinate synthase / 0.715
2hma SAMtRNA-specific 2-thiouridylase MnmA / 0.712
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.710
4jwj SAHtRNA (guanine(9)-N1)-methyltransferase / 0.704
4xfj ANPArgininosuccinate synthase / 0.703
3tw6 ADPPyruvate carboxylase / 0.700
2yy8 SAMtRNA (cytidine(56)-2'-O)-methyltransferase / 0.697
3nk7 SAM23S rRNA (adenosine(1067)-2'-O)-methyltransferase / 0.697
1kh2 ATPArgininosuccinate synthase / 0.696
1mjh ATPUniversal stress protein MJ0577 / 0.694
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.694
1j21 ATPArgininosuccinate synthase / 0.693
2yy8 MTAtRNA (cytidine(56)-2'-O)-methyltransferase / 0.693
5a7y SAHtRNA (adenine(9)-N1)-methyltransferase 2.1.1.218 0.693
3oij SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.692
1j1z ATPArgininosuccinate synthase / 0.691
3hgm ATPTRAP-T-associated universal stress protein TeaD / 0.691
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.691
2ybo SAHMethyltransferase / 0.690
2cx8 SAHRibosomal RNA small subunit methyltransferase E / 0.687
2qbu SAHPrecorrin-2 methyltransferase / 0.687
2npn SAMPutative cobalamin synthesis related protein / 0.684
1kh3 ANPArgininosuccinate synthase / 0.683
2zvb SAHPrecorrin-3 C17-methyltransferase / 0.682
3rv4 ADPBiotin carboxylase 6.3.4.14 0.681
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.679
4x3m ADNRNA 2'-O ribose methyltransferase / 0.676
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.675
3ab8 ATPUncharacterized protein / 0.673
1uam SAHtRNA (guanine-N(1)-)-methyltransferase 2.1.1.228 0.671
2aj4 ANPGalactokinase 2.7.1.6 0.671
4s1h ADPPyridoxal kinase, putative / 0.671
3nut SAHPrecorrin-3 methylase / 0.670
2vqd AP2Biotin carboxylase 6.3.4.14 0.668
4r8h SP1cAMP-activated global transcriptional regulator CRP / 0.668
4ft8 CMPcAMP-activated global transcriptional regulator CRP / 0.666
4jlp ADPAdenylate kinase / 0.666
5c77 SAHProtein arginine N-methyltransferase SFM1 / 0.666
5ahw CMPUniversal stress protein family protein, putative / 0.665
3rk1 ATPN-type ATP pyrophosphatase superfamily / 0.664
4s1b 2BALmo1466 protein / 0.663
4fu0 ADPD-alanine--D-alanine ligase / 0.662
1mxi SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.660
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
4i0b CMPcAMP-activated global transcriptional regulator CRP / 0.660
3qwp SAMHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.659
1v3s ATPSignaling protein / 0.658
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.658
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.658
3bwj ARXcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
2zbv ADNUncharacterized protein / 0.656
1nhk CMPNucleoside diphosphate kinase 2.7.4.6 0.655
4yvh SFGtRNA (guanine-N(1)-)-methyltransferase 2.1.1.228 0.655
3zu0 A12NAD 5'-nucleotidase 3.1.3.5 0.654
4ee3 UDHBeta-1,4-galactosyltransferase 1 / 0.654
1jgt APCCarboxyethyl-arginine beta-lactam-synthase 6.3.3.4 0.653
2z0y SAMRibosomal RNA small subunit methyltransferase E / 0.653
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.651
2j9g ADPBiotin carboxylase 6.3.4.14 0.650
3nie ANPMitogen-activated protein kinase / 0.650