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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
2np6 NEA Modification methylase TaqI 2.1.1.72

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2np6 NEAModification methylase TaqI 2.1.1.72 0.882
2ih2 NEAModification methylase TaqI 2.1.1.72 0.847
2ibt NEAModification methylase TaqI 2.1.1.72 0.846
2np7 NEAModification methylase TaqI 2.1.1.72 0.825
2ih5 NEAModification methylase TaqI 2.1.1.72 0.814
1g38 NEAModification methylase TaqI 2.1.1.72 0.790
1aqi SAHModification methylase TaqI 2.1.1.72 0.729
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.723
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.714
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.712
3ldf SAHUncharacterized protein / 0.709
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.708
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.707
3ldg SAHUncharacterized protein / 0.706
7mht SAHModification methylase HhaI 2.1.1.37 0.705
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.702
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.701
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.698
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.696
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.695
4yac NAIC alpha-dehydrogenase / 0.691
1mht SAHModification methylase HhaI 2.1.1.37 0.690
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.690
2ore SAHDNA adenine methylase 2.1.1.72 0.689
1yf3 SAHDNA adenine methylase / 0.688
3tm4 SAMUncharacterized protein / 0.688
2br5 SAHCephalosporin hydroxylase CmcI / 0.687
3mht SAHModification methylase HhaI 2.1.1.37 0.687
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.686
4kvz SAHPtnL protein / 0.686
1skm SAHModification methylase HhaI 2.1.1.37 0.685
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.685
1boo SAHModification methylase PvuII 2.1.1.113 0.683
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.682
2g1p SAHDNA adenine methylase 2.1.1.72 0.682
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.681
4tm4 FDAKtzI / 0.681
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.680
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.679
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.679
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.677
4mb2 ATPUncharacterized protein / 0.677
10mh SAHModification methylase HhaI 2.1.1.37 0.675
5f8f SFGPossible transcriptional regulatory protein / 0.675
5je3 SAHMethyl transferase / 0.674
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.673
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.671
1eg2 MTAModification methylase RsrI 2.1.1.72 0.670
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.670
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.670
4tlx FDAKtzI / 0.670
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.669
3lsm SFDPyranose 2-oxidase / 0.668
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.668
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.665
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.665
2hms NAIKtr system potassium uptake protein A / 0.664
2ewm NAD(S)-1-Phenylethanol dehydrogenase 1.1.1.311 0.662
2z6u SAHModification methylase HhaI 2.1.1.37 0.662
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.662
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.661
1tdo FADL-amino-acid oxidase 1.4.3.2 0.661
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.660
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.660
2hmv ADPKtr system potassium uptake protein A / 0.660
2p35 SAHTrans-aconitate 2-methyltransferase / 0.660
1nw6 SFGModification methylase RsrI 2.1.1.72 0.659
1wy7 SAHUncharacterized protein / 0.659
2c7q SAHModification methylase HhaI 2.1.1.37 0.659
3k30 ADPHistamine dehydrogenase / 0.659
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.659
3icp NADNAD-dependent epimerase/dehydratase / 0.657
3ko8 NADNAD-dependent epimerase/dehydratase / 0.657
4m55 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.657
4wec NADShort chain dehydrogenase / 0.657
3alm FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.656
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.656
3lsh FADPyranose 2-oxidase / 0.656
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.655
3alj FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.655
3all FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.655
3lsi FADPyranose 2-oxidase / 0.655
3ukf FDAUDP-galactopyranose mutase / 0.655
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.655
4gbe SAHDNA adenine methylase 2.1.1.72 0.655
1zq9 SAMProbable dimethyladenosine transferase / 0.654
2eq7 NADDihydrolipoyl dehydrogenase / 0.654
2yxl SFG450aa long hypothetical fmu protein / 0.654
4id9 NADPutative UDP-glucose 4-epimerase / 0.654
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.654
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.654
5jla NADPutative short-chain dehydrogenase/reductase / 0.654
3rfx NADUronate dehydrogenase / 0.653
2plw SAMRibosomal RNA methyltransferase, putative / 0.652
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.652
4lwp SAHArginine N-methyltransferase, putative / 0.652
2dki FAD3-hydroxybenzoate 4-monooxygenase 1.14.13.23 0.651
2oy0 SAHGenome polyprotein / 0.651
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.651
4guv FADTetX family tetracycline inactivation enzyme / 0.651
4poo SAMPutative RNA methylase / 0.651
2o07 MTASpermidine synthase 2.5.1.16 0.650