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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
3g8a SAH Ribosomal RNA small subunit methyltransferase G

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.887
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.711
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.710
3kkz SAMUncharacterized protein / 0.708
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.702
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.697
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.697
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.695
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.692
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.691
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.690
4lwp SAHArginine N-methyltransferase, putative / 0.690
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.686
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.686
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.685
4c04 SFGProtein arginine N-methyltransferase 6 / 0.685
4nec SAHPutative SAM-dependent methyltransferase / 0.685
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.685
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.684
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.684
5epe SAHUncharacterized protein / 0.684
4c03 SFGProtein arginine N-methyltransferase 6 / 0.683
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.682
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.681
2p35 SAHTrans-aconitate 2-methyltransferase / 0.680
4qpp SAHProtein arginine N-methyltransferase 6 / 0.680
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.679
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.678
5bp7 SAHSAM-dependent methyltransferase / 0.678
3e23 SAMUncharacterized protein / 0.677
4kwc SAHMethyltransferase domain family / 0.677
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.677
5jdz SAHMethyl transferase / 0.676
4fr0 SAMArsenic methyltransferase / 0.675
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.675
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.674
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.674
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.673
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.673
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.673
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.673
3t7s SAMUncharacterized protein / 0.672
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.672
2dki FAD3-hydroxybenzoate 4-monooxygenase 1.14.13.23 0.671
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.671
3t0i SAHPutative methyltransferase / 0.671
3uov FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.671
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.670
2fk8 SAMHydroxymycolate synthase MmaA4 2.1.1 0.669
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.669
3uoy FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.669
3uoz FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.669
1ve3 SAMUncharacterized protein / 0.668
1f3l SAHProtein arginine N-methyltransferase 3 / 0.667
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.667
2qe6 SAMUncharacterized protein / 0.667
2yls FADPhenylacetone monooxygenase 1.14.13.92 0.667
3ict FADCoenzyme A disulfide reductase / 0.666
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.666
4d03 FADPhenylacetone monooxygenase 1.14.13.92 0.666
5je2 SAHMethyl transferase / 0.665
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.664
3uox FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.664
4g6h NAIRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial 1.6.5.9 0.663
2gvc FADThiol-specific monooxygenase 1.14.13 0.662
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.662
1ges FADGlutathione reductase 1.8.1.7 0.661
3fri SAH16S rRNA methylase / 0.661
1eyn 2ANUDP-N-acetylglucosamine 1-carboxyvinyltransferase / 0.660
2xf3 J01Uncharacterized protein / 0.660
2xvv 9DNSerum albumin / 0.660
3cz0 9ODPheromone-binding protein ASP1 / 0.660
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.660
3fo7 IMNPhospholipase A2 VRV-PL-VIIIa / 0.660
3nfa CBJGag-Pol polyprotein / 0.660
3ngq 1PSCCR4-NOT transcription complex subunit 6-like 3.1.13.4 0.660
3nks ACJProtoporphyrinogen oxidase 1.3.3.4 0.660
3q9t FAYUncharacterized protein / 0.660
3t7t SAHUncharacterized protein / 0.660
4c1f X8ZMetallo-beta-lactamase type 2 / 0.660
4ivo ACJProtoporphyrinogen oxidase 1.3.3.4 0.660
4kla CHDFerrochelatase, mitochondrial 4.99.1.1 0.660
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.660
5dby DIFSerum albumin / 0.660
5dby NPSSerum albumin / 0.660
5jqb IBPEnvelope glycoprotein / 0.660
2i0z FADNAD(FAD)-utilizing dehydrogenases / 0.659
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.659
3kkj FADRenalase / 0.659
3ou2 SAHSAM-dependent methyltransferase / 0.659
4emw FADCoenzyme A disulfide reductase / 0.659
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.659
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.659
4uy6 SAHHistidine N-alpha-methyltransferase / 0.659
1skm SAHModification methylase HhaI 2.1.1.37 0.658
5je3 SAHMethyl transferase / 0.658
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.657
2cdu ADPNADH oxidase / 0.657
2yqz SAMUncharacterized protein / 0.657
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.657
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.657
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.656
2xvf FADPutative flavin-containing monooxygenase / 0.656
3cgd FADCoenzyme A disulfide reductase / 0.656
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.656
2c7q SAHModification methylase HhaI 2.1.1.37 0.655
2ylw FADPhenylacetone monooxygenase 1.14.13.92 0.655
3mht SAHModification methylase HhaI 2.1.1.37 0.655
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.655
1cbo 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
1v59 NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.654
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.654
3gyj FADCholesterol oxidase 1.1.3.6 0.654
4b69 FADL-ornithine N(5)-monooxygenase / 0.654
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.654
4rek FADCholesterol oxidase 1.1.3.6 0.654
4tm3 FADKtzI / 0.654
4xwr FADCholesterol oxidase 1.1.3.6 0.654
4xxg FADCholesterol oxidase 1.1.3.6 0.654
5f8f SFGPossible transcriptional regulatory protein / 0.654
1b4v FADCholesterol oxidase 1.1.3.6 0.653
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.653
2gew FADCholesterol oxidase 1.1.3.6 0.653
3hvi 619Catechol O-methyltransferase 2.1.1.6 0.653
3qj4 FADRenalase / 0.653
4eqw FADCoenzyme A disulfide reductase / 0.653
4eqx FADCoenzyme A disulfide reductase / 0.653
4opc FDAConserved Archaeal protein / 0.653
4opd FDAConserved Archaeal protein / 0.653
4tm1 FDAKtzI / 0.653
4tm4 FDAKtzI / 0.653
5bp9 SAHPutative methyltransferase protein / 0.653
2uyh SAHModification methylase HhaI 2.1.1.37 0.652
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.652
3m13 FADMonomeric sarcosine oxidase 1.5.3.1 0.652
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.652
4udr FAD5-(hydroxymethyl)furfural oxidase / 0.652
2c7g FADNADPH-ferredoxin reductase FprA 1.18.1.2 0.651
2hmv ADPKtr system potassium uptake protein A / 0.651
2ym2 FADPhenylacetone monooxygenase 1.14.13.92 0.651
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.651
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.651
1n4u FAECholesterol oxidase 1.1.3.6 0.650
1nhr FADNADH peroxidase 1.11.1.1 0.650
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.650