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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
1b5d DCM Deoxycytidylate 5-hydroxymethyltransferase 2.1.2.8

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1b5d DCMDeoxycytidylate 5-hydroxymethyltransferase 2.1.2.8 1.161
1b5e DCMDeoxycytidylate 5-hydroxymethyltransferase 2.1.2.8 1.147
1f28 UMPThymidylate synthase 2.1.1.45 0.907
5by6 UMPThymidylate synthase / 0.883
4eil UMPBifunctional dihydrofolate reductase-thymidylate synthase 1.5.1.3 0.878
4dq1 UMPThymidylate synthase / 0.873
4ein NOHThymidylate synthase 2.1.1.45 0.865
4isk UMPThymidylate synthase / 0.863
4e5o UMPThymidylate synthase 2.1.1.45 0.856
4irr UMPThymidylate synthase / 0.838
4fox UMPThymidylate synthase ThyA / 0.831
4dpd UMPBifunctional dihydrofolate reductase-thymidylate synthase / 0.826
3dga UMPBifunctional dihydrofolate reductase-thymidylate synthase 1.5.1.3 0.814
3bgx TMPThymidylate synthase / 0.811
2fto TMPThymidylate synthase / 0.807
1tys TMPThymidylate synthase / 0.793
4h0u UMPThymidylate synthase / 0.786
4psg NOHThymidylate synthase / 0.774
4eb4 UMPThymidylate synthase 2.1.1.45 0.766
2tdm UMPThymidylate synthase / 0.763
2g86 UMPThymidylate synthase / 0.761
3dg8 UMPBifunctional dihydrofolate reductase-thymidylate synthase 1.5.1.3 0.758
4iqq UMPThymidylate synthase / 0.750
1nja DCMThymidylate synthase / 0.748
1j3j UMPBifunctional dihydrofolate reductase-thymidylate synthase 1.5.1.3 0.741
1tsy UMPThymidylate synthase / 0.741
1njc DCMThymidylate synthase / 0.738
1vzb UMPThymidylate synthase / 0.738
1njd UMPThymidylate synthase / 0.736
2tsr UMPThymidylate synthase 2.1.1.45 0.735
1jmf UMPThymidylate synthase / 0.729
1tsv UMPThymidylate synthase / 0.726
1tsx UMPThymidylate synthase / 0.724
1bp0 UMPThymidylate synthase / 0.722
2vet UMPThymidylate synthase / 0.719
1vza UMPThymidylate synthase / 0.712
1bp6 UMPThymidylate synthase / 0.711
2g8a UMPThymidylate synthase / 0.708
1bid UMPThymidylate synthase / 0.706
3koy Z97D-ornithine 4,5-aminomutase subunit beta / 0.681
1dap NDPMeso-diaminopimelate D-dehydrogenase 1.4.1.16 0.664
2g89 UMPThymidylate synthase / 0.660
1tdc UMPThymidylate synthase / 0.659
4hs4 FMNChromate reductase / 0.659
1lvg 5GPGuanylate kinase 2.7.4.8 0.658
1jmi UMPThymidylate synthase / 0.657
3hj9 FMNUncharacterized protein / 0.657
1jmh UMPThymidylate synthase / 0.656
1njb UMPThymidylate synthase / 0.655
4bms NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.654
1wur 8DGGTP cyclohydrolase 1 / 0.653
3cx4 ADPGlycogen synthase 2.4.1.21 0.650