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
3rw9 DSH Spermidine synthase 2.5.1.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3rw9 DSHSpermidine synthase 2.5.1.16 0.941
2o06 MTASpermidine synthase 2.5.1.16 0.789
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.771
4yv2 S4MSpermidine synthase, putative / 0.758
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.738
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.731
2o07 MTASpermidine synthase 2.5.1.16 0.731
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.729
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.724
3bwc SAMSpermidine synthase, putative / 0.722
4yuv S4MSpermidine synthase, putative / 0.719
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.716
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.716
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.715
1boo SAHModification methylase PvuII 2.1.1.113 0.706
2hmv ADPKtr system potassium uptake protein A / 0.706
4yuz S4MSpermidine synthase, putative / 0.705
2g1p SAHDNA adenine methylase 2.1.1.72 0.703
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.703
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.702
1yf3 SAHDNA adenine methylase / 0.700
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.700
5je4 SAHMethyl transferase / 0.700
2pt6 S4MSpermidine synthase / 0.699
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.699
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.697
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.696
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.691
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.691
2ih2 NEAModification methylase TaqI 2.1.1.72 0.690
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.688
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.687
4yv0 S4MSpermidine synthase, putative / 0.687
3ou2 SAHSAM-dependent methyltransferase / 0.686
4yv1 S4MSpermidine synthase, putative / 0.686
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.685
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.684
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.684
1orr NADCDP-paratose 2-epimerase / 0.683
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.683
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.682
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.681
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.681
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.681
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.681
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.679
4b65 FADL-ornithine N(5)-monooxygenase / 0.679
4poo SAMPutative RNA methylase / 0.679
3kkz SAMUncharacterized protein / 0.678
1g38 NEAModification methylase TaqI 2.1.1.72 0.677
1ve3 SAMUncharacterized protein / 0.677
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.677
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.676
4tlx FDAKtzI / 0.676
5je2 SAHMethyl transferase / 0.676
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.675
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.674
2np7 NEAModification methylase TaqI 2.1.1.72 0.674
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.674
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.673
3mht SAHModification methylase HhaI 2.1.1.37 0.673
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.673
5cku FADL-ornithine N(5)-monooxygenase / 0.673
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.672
4tm4 FDAKtzI / 0.672
4yac NAIC alpha-dehydrogenase / 0.672
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.670
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.669
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.669
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.669
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.669
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.669
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.668
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.668
4nec SAHPutative SAM-dependent methyltransferase / 0.668
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.668
1aqi SAHModification methylase TaqI 2.1.1.72 0.667
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.667
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.667
3he3 FADUDP-galactopyranose mutase / 0.667
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.667
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.667
4rvd SAMD-mycarose 3-C-methyltransferase / 0.666
2ore SAHDNA adenine methylase 2.1.1.72 0.665
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.665
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.664
2fje FADAdenylylsulfate reductase, subunit A (AprA) / 0.664
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.664
5hxw FADL-amino acid deaminase / 0.664
1nw5 SAMModification methylase RsrI 2.1.1.72 0.663
1wy7 SAHUncharacterized protein / 0.663
3ko8 NADNAD-dependent epimerase/dehydratase / 0.663
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.662
3lby SAHUncharacterized protein / 0.662
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.661
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.661
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.660
2zfu SAHRibosomal RNA-processing protein 8 / 0.660
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.660
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.660
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.660
3ka7 FADPutative oxidoreductase / 0.659
3vyw SAMUncharacterized protein / 0.659
5d4v SAHUncharacterized protein MJ0489 / 0.659
7mht SAHModification methylase HhaI 2.1.1.37 0.659
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.658
3ou7 SAMSAM-dependent methyltransferase / 0.658
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.657
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.657
4jdr FADDihydrolipoyl dehydrogenase 1.8.1.4 0.657
4kwc SAHMethyltransferase domain family / 0.656
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.655
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.655
2yxl SFG450aa long hypothetical fmu protein / 0.654
4tm1 FDAKtzI / 0.654
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.654
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.653
2hnk SAHSAM-dependent O-methyltransferase / 0.653
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.653
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.653
1nw6 SFGModification methylase RsrI 2.1.1.72 0.651
3oe4 610Catechol O-methyltransferase 2.1.1.6 0.651
2hms NAIKtr system potassium uptake protein A / 0.650
3iv6 SAMUncharacterized protein / 0.650
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.650
4b69 FADL-ornithine N(5)-monooxygenase / 0.650