Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
3v8v SAM Ribosomal RNA large subunit methyltransferase K/L 2.1.1.173

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 1.076
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.839
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.764
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.761
3duw SAHO-methyltransferase, putative / 0.750
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.748
2hnk SAHSAM-dependent O-methyltransferase / 0.743
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.736
3vyw SAMUncharacterized protein / 0.733
1yf3 SAHDNA adenine methylase / 0.732
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.731
1nw6 SFGModification methylase RsrI 2.1.1.72 0.730
2yxl SFG450aa long hypothetical fmu protein / 0.729
3ldg SAHUncharacterized protein / 0.727
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.723
3tos SAHCalS11 / 0.721
3oe4 610Catechol O-methyltransferase 2.1.1.6 0.718
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.717
3ou2 SAHSAM-dependent methyltransferase / 0.716
5je4 SAHMethyl transferase / 0.716
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.714
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.713
5jdz SAHMethyl transferase / 0.713
5je3 SAHMethyl transferase / 0.712
2g1p SAHDNA adenine methylase 2.1.1.72 0.709
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.706
1wy7 SAHUncharacterized protein / 0.705
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.705
1nw5 SAMModification methylase RsrI 2.1.1.72 0.704
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.704
2i9k SAHModification methylase HhaI 2.1.1.37 0.703
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.703
3ldf SAHUncharacterized protein / 0.703
4yuz S4MSpermidine synthase, putative / 0.703
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.700
3s55 NADPutative short-chain dehydrogenase/reductase / 0.700
2pan FADGlyoxylate carboligase 4.1.1.47 0.697
1eg2 MTAModification methylase RsrI 2.1.1.72 0.696
1txz APRProbable ADP-ribose 1''-phosphate phosphatase YML087W 3.1.3.84 0.695
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.694
2o06 MTASpermidine synthase 2.5.1.16 0.690
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.690
5f8f SFGPossible transcriptional regulatory protein / 0.687
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.686
4gbe SAHDNA adenine methylase 2.1.1.72 0.686
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.686
4yv2 S4MSpermidine synthase, putative / 0.686
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.685
4gf5 SAHCalS11 / 0.685
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.685
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.684
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.683
4yag NAIC alpha-dehydrogenase / 0.683
3tm4 SAMUncharacterized protein / 0.682
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.681
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.681
2ibt NEAModification methylase TaqI 2.1.1.72 0.681
2plw SAMRibosomal RNA methyltransferase, putative / 0.681
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.681
1yqz FADCoenzyme A disulfide reductase / 0.680
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.680
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.679
2np6 NEAModification methylase TaqI 2.1.1.72 0.679
4dkj SAHCytosine-specific methyltransferase / 0.679
4poo SAMPutative RNA methylase / 0.679
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.678
3c3y SAHO-methyltransferase / 0.677
4yac NAIC alpha-dehydrogenase / 0.677
5je2 SAHMethyl transferase / 0.675
3ou7 SAMSAM-dependent methyltransferase / 0.674
3geg NADShort-chain dehydrogenase/reductase SDR / 0.673
3ou6 SAMSAM-dependent methyltransferase / 0.673
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.672
2np7 NEAModification methylase TaqI 2.1.1.72 0.671
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.670
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.670
2z6u SAHModification methylase HhaI 2.1.1.37 0.670
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.669
3hvi 619Catechol O-methyltransferase 2.1.1.6 0.669
3rw9 DSHSpermidine synthase 2.5.1.16 0.669
4em4 FADCoenzyme A disulfide reductase / 0.669
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.669
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.668
2c7q SAHModification methylase HhaI 2.1.1.37 0.668
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.668
3cbg SAHO-methyltransferase / 0.667
3ict FADCoenzyme A disulfide reductase / 0.667
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.667
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.667
4rtk SAHDNA adenine methylase 2.1.1.72 0.667
3vaq ADNPutative adenosine kinase / 0.665
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.665
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.664
2cww SAHUncharacterized protein / 0.664
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.664
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.664
5bw4 SAMUncharacterized protein / 0.664
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.664
2zcj SAHModification methylase HhaI 2.1.1.37 0.663
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.662
4dc3 2FAPutative adenosine kinase / 0.662
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.662
1y56 ATPUncharacterized protein / 0.661
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.661
2ih5 NEAModification methylase TaqI 2.1.1.72 0.660
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.659
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.659
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.658
4rtj SFGDNA adenine methylase 2.1.1.72 0.657
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.656
4oa5 SAHO-methyltransferase family protein / 0.656
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.655
2f8l SAMLmo1582 protein / 0.655
2h39 ADQADP-glucose phosphorylase / 0.655
3iv6 SAMUncharacterized protein / 0.655
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.655
2iwh ANPElongation factor 3A / 0.653
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.652
1boo SAHModification methylase PvuII 2.1.1.113 0.651
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.651
4kwc SAHMethyltransferase domain family / 0.651
4rtr SAMDNA adenine methylase 2.1.1.72 0.651
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.651
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.651
2ih2 NEAModification methylase TaqI 2.1.1.72 0.650
4mb2 ATPUncharacterized protein / 0.650