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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
2ibt NEA Modification methylase TaqI 2.1.1.72

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2ibt NEAModification methylase TaqI 2.1.1.72 0.928
2np7 NEAModification methylase TaqI 2.1.1.72 0.894
2ih2 NEAModification methylase TaqI 2.1.1.72 0.886
2ih5 NEAModification methylase TaqI 2.1.1.72 0.866
2np6 NEAModification methylase TaqI 2.1.1.72 0.846
1g38 NEAModification methylase TaqI 2.1.1.72 0.845
5jdz SAHMethyl transferase / 0.756
5je3 SAHMethyl transferase / 0.756
5je4 SAHMethyl transferase / 0.743
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.734
2c7q SAHModification methylase HhaI 2.1.1.37 0.729
2o06 MTASpermidine synthase 2.5.1.16 0.729
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.728
4yv2 S4MSpermidine synthase, putative / 0.727
4nec SAHPutative SAM-dependent methyltransferase / 0.723
7mht SAHModification methylase HhaI 2.1.1.37 0.718
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.717
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.717
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.715
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.712
5je2 SAHMethyl transferase / 0.711
1aqi SAHModification methylase TaqI 2.1.1.72 0.710
2uyh SAHModification methylase HhaI 2.1.1.37 0.709
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.709
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.709
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.708
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.705
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.704
3ldg SAHUncharacterized protein / 0.704
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.702
3ldf SAHUncharacterized protein / 0.702
4hh4 SAHCcbJ / 0.702
1y9d FADPyruvate oxidase 1.2.3.3 0.701
2g1p SAHDNA adenine methylase 2.1.1.72 0.701
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.701
1skm SAHModification methylase HhaI 2.1.1.37 0.699
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.699
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.691
4yv0 S4MSpermidine synthase, putative / 0.691
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.691
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.691
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.689
4b69 FADL-ornithine N(5)-monooxygenase / 0.689
4nzh FADL-ornithine N(5)-monooxygenase / 0.688
1mht SAHModification methylase HhaI 2.1.1.37 0.686
5bxy SAHPutative RNA methylase family UPF0020 / 0.685
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.684
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.683
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.681
3fpf MTAUncharacterized protein / 0.679
5f8f SFGPossible transcriptional regulatory protein / 0.678
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.677
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.677
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.676
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.675
3lsm SFDPyranose 2-oxidase / 0.675
4rtk SAHDNA adenine methylase 2.1.1.72 0.674
3c3y SAHO-methyltransferase / 0.673
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.673
4gbe SAHDNA adenine methylase 2.1.1.72 0.673
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.673
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.672
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.672
5bp9 SAHPutative methyltransferase protein / 0.672
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.671
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.671
1zk7 FADMercuric reductase 1.16.1.1 0.671
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.671
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.671
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.670
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.669
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.669
2ore SAHDNA adenine methylase 2.1.1.72 0.669
3ad9 FADSubunit beta of sarcosine oxidase / 0.669
3fri SAH16S rRNA methylase / 0.669
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.669
2br5 SAHCephalosporin hydroxylase CmcI / 0.668
2f8l SAMLmo1582 protein / 0.668
2p5u NADUDP-glucose 4-epimerase / 0.668
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.668
3he3 FADUDP-galactopyranose mutase / 0.668
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.668
4wec NADShort chain dehydrogenase / 0.668
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.667
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.667
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.667
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.667
4tm4 FDAKtzI / 0.667
3t7s SAMUncharacterized protein / 0.666
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.665
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.664
2gs9 SAHUncharacterized protein / 0.664
2q7v FADThioredoxin reductase / 0.664
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.664
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.663
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.663
5hxw FADL-amino acid deaminase / 0.663
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.662
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.662
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.661
1ori SAHProtein arginine N-methyltransferase 1 / 0.660
1zmc FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.660
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.660
1g60 SAMModification methylase MboII 2.1.1.72 0.659
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.657
3alj FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.657
3e23 SAMUncharacterized protein / 0.657
3n1s 5GPPurine nucleoside phosphoramidase / 0.657
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.657
4rtq SAHDNA adenine methylase 2.1.1.72 0.657
4yac NAIC alpha-dehydrogenase / 0.657
2c20 NADUDP-glucose 4-epimerase / 0.656
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.656
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.656
4rpg FADUDP-galactopyranose mutase 5.4.99.9 0.656
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.656
4fr0 SAMArsenic methyltransferase / 0.654
3rfx NADUronate dehydrogenase / 0.653
4kwc SAHMethyltransferase domain family / 0.653
3oz2 FADDigeranylgeranylglycerophospholipid reductase / 0.652
4c04 SFGProtein arginine N-methyltransferase 6 / 0.652
5ahk FADAcetolactate synthase II, large subunit / 0.652
2yxl SFG450aa long hypothetical fmu protein / 0.651
1uay ADNOxidoreductase / 0.650
3kkz SAMUncharacterized protein / 0.650
3tlj SAHUncharacterized protein / 0.650
4gf5 SAHCalS11 / 0.650