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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
4cng SAH SpoU rRNA methylase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4cng SAHSpoU rRNA methylase / 0.990
4cnf MTASpoU rRNA methylase / 0.914
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.836
4kgn SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.799
4jal SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.780
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.776
2ha8 SAHProbable methyltransferase TARBP1 / 0.775
3n4k SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.770
4x3l MTARNA 2'-O ribose methyltransferase / 0.746
1mxi SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.744
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.737
3gyq SAM23S rRNA (adenosine(1067)-2'-O)-methyltransferase / 0.736
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.728
3tw6 ADPPyruvate carboxylase / 0.728
4jwh SAHtRNA (guanine(9)-N1)-methyltransferase / 0.725
4xbo SAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ 2.1.1.200 0.723
2yy8 MTAtRNA (cytidine(56)-2'-O)-methyltransferase / 0.719
2yy8 SAMtRNA (cytidine(56)-2'-O)-methyltransferase / 0.717
4ig6 SAHtRNA (guanine-N(1)-)-methyltransferase / 0.713
2cx8 SAHRibosomal RNA small subunit methyltransferase E / 0.704
5a7y SAHtRNA (adenine(9)-N1)-methyltransferase 2.1.1.218 0.704
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.695
1kor ANPArgininosuccinate synthase / 0.693
2z08 ATPUniversal stress protein family / 0.692
4xfj ANPArgininosuccinate synthase / 0.691
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.690
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.686
2vqd AP2Biotin carboxylase 6.3.4.14 0.686
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.686
2qmm SAMtRNA (pseudouridine(54)-N(1))-methyltransferase / 0.685
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.684
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.683
1kp2 ATPArgininosuccinate synthase 6.3.4.5 0.682
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.682
3nk7 SAM23S rRNA (adenosine(1067)-2'-O)-methyltransferase / 0.680
1mjh ATPUniversal stress protein MJ0577 / 0.679
3wnz ADPAlanine--anticapsin ligase / 0.678
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.678
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.676
4jwj SAHtRNA (guanine(9)-N1)-methyltransferase / 0.676
4x3m ADNRNA 2'-O ribose methyltransferase / 0.675
1nhk CMPNucleoside diphosphate kinase 2.7.4.6 0.673
1j21 ATPArgininosuccinate synthase / 0.672
2ejz SAHDiphthine synthase / 0.672
3rv4 ADPBiotin carboxylase 6.3.4.14 0.670
1kh2 ATPArgininosuccinate synthase / 0.667
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.667
2zvc SAHPrecorrin-3 C17-methyltransferase / 0.666
2z0y SAMRibosomal RNA small subunit methyltransferase E / 0.665
3ab8 ATPUncharacterized protein / 0.665
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.665
5cns DATRibonucleoside-diphosphate reductase 1 subunit alpha 1.17.4.1 0.665
1v9a SAHUncharacterized protein / 0.664
2zvb SAHPrecorrin-3 C17-methyltransferase / 0.664
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.664
3bbh SFGRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.663
4r8h SP1cAMP-activated global transcriptional regulator CRP / 0.663
2ybo SAHMethyltransferase / 0.662
5c77 SAHProtein arginine N-methyltransferase SFM1 / 0.662
2z6r SAHDiphthine synthase / 0.661
3g8d ADPBiotin carboxylase 6.3.4.14 0.660
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.660
5c1p ADPD-alanine--D-alanine ligase / 0.660
2e15 SAHDiphthine synthase / 0.659
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.659
1pk8 ATPSynapsin-1 / 0.658
4fu0 ADPD-alanine--D-alanine ligase / 0.658
1s4d SAHUroporphyrinogen-III C-methyltransferase 2.1.1.107 0.657
2xul ATPNitrogen regulatory protein P-II / 0.657
4yvg SAMtRNA (guanine-N(1)-)-methyltransferase 2.1.1.228 0.657
2qbu SAHPrecorrin-2 methyltransferase / 0.656
3mhy ATPNitrogen regulatory protein P-II 1 / 0.655
4ib3 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.655
1uam SAHtRNA (guanine-N(1)-)-methyltransferase 2.1.1.228 0.654
1v3s ATPSignaling protein / 0.654
1ia9 ANPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.653
2j9g ANPBiotin carboxylase 6.3.4.14 0.652
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.652
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
2ejj SAHDiphthine synthase / 0.650
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.650