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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
3ldg SAH Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3ldg SAHUncharacterized protein / 0.971
1nw5 SAMModification methylase RsrI 2.1.1.72 0.814
1boo SAHModification methylase PvuII 2.1.1.113 0.790
1g60 SAMModification methylase MboII 2.1.1.72 0.785
3tm4 SAMUncharacterized protein / 0.785
2c7q SAHModification methylase HhaI 2.1.1.37 0.773
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.769
2zcj SAHModification methylase HhaI 2.1.1.37 0.767
3mht SAHModification methylase HhaI 2.1.1.37 0.767
2f8l SAMLmo1582 protein / 0.764
2i9k SAHModification methylase HhaI 2.1.1.37 0.763
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.757
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.756
1eg2 MTAModification methylase RsrI 2.1.1.72 0.754
1skm SAHModification methylase HhaI 2.1.1.37 0.754
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.753
2uyh SAHModification methylase HhaI 2.1.1.37 0.751
4rtk SAHDNA adenine methylase 2.1.1.72 0.751
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.743
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.742
2z6u SAHModification methylase HhaI 2.1.1.37 0.740
3tm5 SFGUncharacterized protein / 0.738
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.738
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.737
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.735
5jdz SAHMethyl transferase / 0.735
10mh SAHModification methylase HhaI 2.1.1.37 0.734
2ore SAHDNA adenine methylase 2.1.1.72 0.734
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.732
2g1p SAHDNA adenine methylase 2.1.1.72 0.730
4rtj SFGDNA adenine methylase 2.1.1.72 0.730
1fjx SAHModification methylase HhaI 2.1.1.37 0.728
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.727
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.726
2o07 MTASpermidine synthase 2.5.1.16 0.720
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.720
3ou2 SAHSAM-dependent methyltransferase / 0.719
7mht SAHModification methylase HhaI 2.1.1.37 0.719
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.717
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.716
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.716
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.715
2zif SAMMethyltransferase / 0.715
4dkj SAHCytosine-specific methyltransferase / 0.714
5je3 SAHMethyl transferase / 0.714
3cbg SAHO-methyltransferase / 0.712
3tos SAHCalS11 / 0.712
5f8f SFGPossible transcriptional regulatory protein / 0.712
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.708
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.708
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.708
4poo SAMPutative RNA methylase / 0.708
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.707
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.707
3tlj SAHUncharacterized protein / 0.707
2np6 NEAModification methylase TaqI 2.1.1.72 0.706
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.705
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.705
4rtr SAMDNA adenine methylase 2.1.1.72 0.705
2ibt NEAModification methylase TaqI 2.1.1.72 0.704
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.703
2yxl SFG450aa long hypothetical fmu protein / 0.702
3qv2 SAH5-cytosine DNA methyltransferase / 0.702
4mht SAHModification methylase HhaI 2.1.1.37 0.702
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.701
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.701
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.701
4ft4 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.700
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.699
4rtq SAHDNA adenine methylase 2.1.1.72 0.699
4c03 SFGProtein arginine N-methyltransferase 6 / 0.697
4kvz SAHPtnL protein / 0.697
1nw6 SFGModification methylase RsrI 2.1.1.72 0.696
1yf3 SAHDNA adenine methylase / 0.695
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.695
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.693
4rtm SAMDNA adenine methylase 2.1.1.72 0.693
3go4 SAHUncharacterized protein / 0.692
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.691
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.691
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.690
4yv2 S4MSpermidine synthase, putative / 0.690
2ih2 NEAModification methylase TaqI 2.1.1.72 0.689
4gbe SAHDNA adenine methylase 2.1.1.72 0.689
4rts SAMDNA adenine methylase 2.1.1.72 0.688
3swr SFGDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.687
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.686
3iv6 SAMUncharacterized protein / 0.685
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.683
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.683
4xba 5GPAprataxin-like protein 3 0.683
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.682
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.682
4rto SFGDNA adenine methylase 2.1.1.72 0.682
2hmv ADPKtr system potassium uptake protein A / 0.681
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.681
4dmg SAMUncharacterized protein / 0.681
1aqi SAHModification methylase TaqI 2.1.1.72 0.680
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.680
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.679
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.679
4kwc SAHMethyltransferase domain family / 0.679
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.677
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.677
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.676
2np7 NEAModification methylase TaqI 2.1.1.72 0.676
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.675
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.675
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.675
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.674
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.674
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.674
1wy7 SAHUncharacterized protein / 0.673
1x1c SAHC-20 methyltransferase / 0.673
2hms NAIKtr system potassium uptake protein A / 0.673
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.673
4tm3 FADKtzI / 0.673
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.672
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.672
1yc2 APRNAD-dependent protein deacylase 2 / 0.671
3fri SAH16S rRNA methylase / 0.671
1mht SAHModification methylase HhaI 2.1.1.37 0.670
2hmy SAMModification methylase HhaI 2.1.1.37 0.670
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.668
2o06 MTASpermidine synthase 2.5.1.16 0.668
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.668
2fkn NADUrocanate hydratase 4.2.1.49 0.667
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.665
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.664
9mht SAHModification methylase HhaI 2.1.1.37 0.664
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.663
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.663
5je2 SAHMethyl transferase / 0.663
8mht SAHModification methylase HhaI 2.1.1.37 0.663
3eey SAMrRNA methylase / 0.662
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.662
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.661
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.660
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.659
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.658
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.658
3c3y SAHO-methyltransferase / 0.658
4k6m SAHGenome polyprotein / 0.658
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.657
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.657
1ptj SNDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.657
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.657
4u8p FDAUDP-galactopyranose mutase / 0.657
4uck SAMLarge structural protein / 0.656
3m6v SAMRibosomal RNA small subunit methyltransferase F / 0.655
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.654
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.654
4rtp SAMDNA adenine methylase 2.1.1.72 0.654
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.653
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.653
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.653
4rtl SFGDNA adenine methylase 2.1.1.72 0.653
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.652
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.652
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.652
4fr0 SAMArsenic methyltransferase / 0.652
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.652
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.652
1g38 NEAModification methylase TaqI 2.1.1.72 0.650