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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
2hv9 SFG 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
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 1.036
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.884
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.864
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.842
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.840
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.819
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.795
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.791
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.777
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.776
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.775
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.770
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.763
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.762
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.761
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.757
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.757
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.756
2zfu SAHRibosomal RNA-processing protein 8 / 0.754
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.753
4hh4 SAHCcbJ / 0.752
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.744
4nec SAHPutative SAM-dependent methyltransferase / 0.743
5jdz SAHMethyl transferase / 0.743
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.741
3fri SAH16S rRNA methylase / 0.739
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.736
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.735
4qpp SAHProtein arginine N-methyltransferase 6 / 0.735
1ve3 SAMUncharacterized protein / 0.734
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.730
2p35 SAHTrans-aconitate 2-methyltransferase / 0.727
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.725
5bp9 SAHPutative methyltransferase protein / 0.722
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.721
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.720
3kkz SAMUncharacterized protein / 0.720
4kwc SAHMethyltransferase domain family / 0.719
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.715
5je3 SAHMethyl transferase / 0.714
3p9k SAHCaffeic acid O-methyltransferase / 0.713
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.713
3p9c SAHCaffeic acid O-methyltransferase / 0.712
2yqz SAMUncharacterized protein / 0.711
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.711
4c03 SFGProtein arginine N-methyltransferase 6 / 0.711
1f3l SAHProtein arginine N-methyltransferase 3 / 0.710
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.710
3e23 SAMUncharacterized protein / 0.708
5f8f SFGPossible transcriptional regulatory protein / 0.708
5je2 SAHMethyl transferase / 0.708
3t7s SAMUncharacterized protein / 0.706
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.705
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.703
3lcc SAHThiocyanate methyltransferase 1 / 0.701
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.699
4kvz SAHPtnL protein / 0.698
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.695
3ou2 SAHSAM-dependent methyltransferase / 0.694
3t0i SAHPutative methyltransferase / 0.694
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.693
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.692
4rtk SAHDNA adenine methylase 2.1.1.72 0.692
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.690
5epe SAHUncharacterized protein / 0.689
2o06 MTASpermidine synthase 2.5.1.16 0.688
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.688
4yv1 S4MSpermidine synthase, putative / 0.685
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.684
2ibt NEAModification methylase TaqI 2.1.1.72 0.684
4yuv S4MSpermidine synthase, putative / 0.683
2ih2 NEAModification methylase TaqI 2.1.1.72 0.682
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.682
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.682
4qnu GEKtRNA U34 carboxymethyltransferase / 0.682
3dh0 SAMUncharacterized protein / 0.680
4yuz S4MSpermidine synthase, putative / 0.680
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.680
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.679
4qnv GEKtRNA U34 carboxymethyltransferase / 0.679
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.677
4fr0 SAMArsenic methyltransferase / 0.677
5f2k SAHUncharacterized protein / 0.677
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.676
3t7t SAHUncharacterized protein / 0.676
5bp7 SAHSAM-dependent methyltransferase / 0.676
2yxl SFG450aa long hypothetical fmu protein / 0.675
3bwc SAMSpermidine synthase, putative / 0.674
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.674
3ldg SAHUncharacterized protein / 0.673
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.671
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.671
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.671
3go4 SAHUncharacterized protein / 0.671
1wy7 SAHUncharacterized protein / 0.670
4pne SAHMethyltransferase-like protein / 0.670
4rtj SFGDNA adenine methylase 2.1.1.72 0.670
2g1p SAHDNA adenine methylase 2.1.1.72 0.669
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.669
4yv2 S4MSpermidine synthase, putative / 0.669
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.668
3sxj SAMPutative methyltransferase / 0.668
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.667
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.666
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.666
4c04 SFGProtein arginine N-methyltransferase 6 / 0.666
4rvd SAMD-mycarose 3-C-methyltransferase / 0.666
1orh SAHProtein arginine N-methyltransferase 1 / 0.665
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.665
4e2x SAHMethyltransferase / 0.664
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.664
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.663
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.663
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.662
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.661
2qe6 SAMUncharacterized protein / 0.661
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.661
4wec NADShort chain dehydrogenase / 0.661
5bxy SAHPutative RNA methylase family UPF0020 / 0.661
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.661
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.660
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.660
3rfx NADUronate dehydrogenase / 0.660
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.660
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.659
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.659
3tm4 SAMUncharacterized protein / 0.659
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.658
3bg7 FADPyranose 2-oxidase / 0.658
3hvi 619Catechol O-methyltransferase 2.1.1.6 0.658
3lst SAHCalO1 / 0.658
2np7 NEAModification methylase TaqI 2.1.1.72 0.657
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.657
9mht SAHModification methylase HhaI 2.1.1.37 0.657
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.656
1x1a SAMC-20 methyltransferase / 0.655
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.655
1b8s FADCholesterol oxidase 1.1.3.6 0.654
1mxt FAECholesterol oxidase 1.1.3.6 0.654
1n1p FADCholesterol oxidase 1.1.3.6 0.654
1n4v FADCholesterol oxidase 1.1.3.6 0.654
1n4w FADCholesterol oxidase 1.1.3.6 0.654
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.654
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.654
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.654
4xxg FADCholesterol oxidase 1.1.3.6 0.654
2xvm SAHTellurite methyltransferase 2.1.1.265 0.653
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.653
4rtr SAMDNA adenine methylase 2.1.1.72 0.653
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.652
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.652
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.652
3tza TZGGlutamate receptor 2 / 0.652
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.652
1wam FADUDP-galactopyranose mutase 5.4.99.9 0.650
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.650