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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
2npn SAM Putative cobalamin synthesis related protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2npn SAMPutative cobalamin synthesis related protein / 1.089
3nd1 SAHPrecorrin-6A synthase (Deacetylating) / 0.947
1s4d SAHUroporphyrinogen-III C-methyltransferase 2.1.1.107 0.844
3ndc SAHPrecorrin-4 C(11)-methyltransferase 2.1.1.133 0.826
2qbu SAHPrecorrin-2 methyltransferase / 0.801
3nut SAHPrecorrin-3 methylase / 0.800
2zvb SAHPrecorrin-3 C17-methyltransferase / 0.798
2zvc SAHPrecorrin-3 C17-methyltransferase / 0.792
2ybo SAHMethyltransferase / 0.784
1cbf SAHCobalt-precorrin-4 C(11)-methyltransferase 2.1.1.271 0.741
1v9a SAHUncharacterized protein / 0.716
1j1z ATPArgininosuccinate synthase / 0.687
2bb3 SAHCobalamin biosynthesis precorrin-6Y methylase (CbiE) / 0.686
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.684
4cnf MTASpoU rRNA methylase / 0.680
1kh2 ATPArgininosuccinate synthase / 0.679
1mjh ATPUniversal stress protein MJ0577 / 0.677
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.677
4prx ADPDNA gyrase subunit B / 0.677
1kh3 ANPArgininosuccinate synthase / 0.675
1g8o U5PN-acetyllactosaminide alpha-1,3-galactosyltransferase / 0.671
3zu0 A12NAD 5'-nucleotidase 3.1.3.5 0.671
1s16 ANPDNA topoisomerase 4 subunit B / 0.670
4xfj ANPArgininosuccinate synthase / 0.670
2hma SAMtRNA-specific 2-thiouridylase MnmA / 0.669
2ejz SAHDiphthine synthase / 0.667
2e0n SAHPrecorrin-2 C20-methyltransferase / 0.665
2p6d SAHDiphthine synthase / 0.663
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.663
4wud ANPDNA gyrase subunit B / 0.662
3ab8 ATPUncharacterized protein / 0.659
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.656
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
2z08 ATPUniversal stress protein family / 0.656
2d1t SLULuciferin 4-monooxygenase 1.13.12.7 0.654
2owf SAHDiphthine synthase / 0.651
1cgp CMPcAMP-activated global transcriptional regulator CRP / 0.650
1kp3 ATPArgininosuccinate synthase 6.3.4.5 0.650