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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
1z3c SA8 mRNA cap guanine-N7 methyltransferase 2.1.1.56

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.965
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.884
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.880
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.827
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.790
1ve3 SAMUncharacterized protein / 0.785
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.776
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.774
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.766
5je3 SAHMethyl transferase / 0.754
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.752
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.742
5jdz SAHMethyl transferase / 0.739
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.738
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.738
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.718
3e23 SAMUncharacterized protein / 0.716
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.714
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.712
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.709
2xvm SAHTellurite methyltransferase 2.1.1.265 0.707
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.706
5bp7 SAHSAM-dependent methyltransferase / 0.705
4pne SAHMethyltransferase-like protein / 0.704
3ou2 SAHSAM-dependent methyltransferase / 0.703
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.702
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.702
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.701
2p35 SAHTrans-aconitate 2-methyltransferase / 0.700
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.700
3go4 SAHUncharacterized protein / 0.700
5epe SAHUncharacterized protein / 0.699
4nec SAHPutative SAM-dependent methyltransferase / 0.698
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.698
4kvz SAHPtnL protein / 0.697
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.696
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.696
2o06 MTASpermidine synthase 2.5.1.16 0.694
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.693
3t0i SAHPutative methyltransferase / 0.692
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.690
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.687
2yqz SAMUncharacterized protein / 0.687
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.687
4hh4 SAHCcbJ / 0.685
2eg5 SAH7-methylxanthosine synthase 1 / 0.684
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.684
3ldg SAHUncharacterized protein / 0.683
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.682
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.682
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.682
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.682
2zfu SAHRibosomal RNA-processing protein 8 / 0.681
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.681
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.681
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.679
2ih5 NEAModification methylase TaqI 2.1.1.72 0.678
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.678
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.678
2br5 SAHCephalosporin hydroxylase CmcI / 0.677
5bp9 SAHPutative methyltransferase protein / 0.677
5f2k SAHUncharacterized protein / 0.677
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.676
1rzy 5ASHistidine triad nucleotide-binding protein 1 3 0.675
3t7s SAMUncharacterized protein / 0.675
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.675
4lwp SAHArginine N-methyltransferase, putative / 0.675
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.675
2c7q SAHModification methylase HhaI 2.1.1.37 0.674
2np7 NEAModification methylase TaqI 2.1.1.72 0.674
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.674
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.673
2f8l SAMLmo1582 protein / 0.672
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.672
3p9c SAHCaffeic acid O-methyltransferase / 0.672
4qpp SAHProtein arginine N-methyltransferase 6 / 0.672
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.672
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.671
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.671
2ih2 NEAModification methylase TaqI 2.1.1.72 0.670
3fri SAH16S rRNA methylase / 0.670
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.670
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.669
2ibt NEAModification methylase TaqI 2.1.1.72 0.669
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.667
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.667
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.667
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.666
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.666
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.666
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.666
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.666
3lst SAHCalO1 / 0.665
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.664
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.664
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.664
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.664
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.663
4dkj SAHCytosine-specific methyltransferase / 0.663
4yuz S4MSpermidine synthase, putative / 0.663
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.663
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.662
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.661
5je4 SAHMethyl transferase / 0.661
7mht SAHModification methylase HhaI 2.1.1.37 0.661
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.660
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.659
3bg7 FADPyranose 2-oxidase / 0.659
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.659
1skm SAHModification methylase HhaI 2.1.1.37 0.658
2hmy SAMModification methylase HhaI 2.1.1.37 0.658
3lcc SAHThiocyanate methyltransferase 1 / 0.658
4rvd SAMD-mycarose 3-C-methyltransferase / 0.658
5cku FADL-ornithine N(5)-monooxygenase / 0.658
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.657
3lsh FADPyranose 2-oxidase / 0.657
1mxt FAECholesterol oxidase 1.1.3.6 0.656
1n4w FADCholesterol oxidase 1.1.3.6 0.656
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.656
4rek FADCholesterol oxidase 1.1.3.6 0.656
4xwr FADCholesterol oxidase 1.1.3.6 0.656
4xxg FADCholesterol oxidase 1.1.3.6 0.656
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.655
2i9k SAHModification methylase HhaI 2.1.1.37 0.655
2z6u SAHModification methylase HhaI 2.1.1.37 0.655
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.655
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.655
9mht SAHModification methylase HhaI 2.1.1.37 0.655
1g38 NEAModification methylase TaqI 2.1.1.72 0.654
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.654
3lsm SFDPyranose 2-oxidase / 0.654
3nlc FADUncharacterized protein / 0.654
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.654
3rw9 DSHSpermidine synthase 2.5.1.16 0.653
4b63 FADL-ornithine N(5)-monooxygenase / 0.653
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.652
2ore SAHDNA adenine methylase 2.1.1.72 0.652
3gu3 SAHMethyltransferase / 0.652
1f3l SAHProtein arginine N-methyltransferase 3 / 0.651
2bra FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.651
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.651
3mht SAHModification methylase HhaI 2.1.1.37 0.651
5bxy SAHPutative RNA methylase family UPF0020 / 0.651
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.651
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.650