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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
3pz3 PZ3 Geranylgeranyl transferase type-2 subunit beta 2.5.1.60

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3pz3 PZ3Geranylgeranyl transferase type-2 subunit beta 2.5.1.60 0.839
2bri ANPUridylate kinase 2.7.4.22 0.744
2xi3 GTPGenome polyprotein 2.7.7.48 0.744
2zue ANPArginine--tRNA ligase 6.1.1.19 0.744
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.744
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.744
4g01 GDPRas-related protein RABF2b / 0.744
4jjz ADPFormate--tetrahydrofolate ligase / 0.744
4ldj GDPGTPase KRas / 0.744
4o3m ADPBloom syndrome protein 3.6.4.12 0.744
4obe GDPGTPase KRas / 0.744
4yqf GDPSeptin-9 / 0.744
4z17 PEPEnolase / 0.744
4z54 GDPNeuronal-specific septin-3 / 0.744
5cyo GDPSeptin-9 / 0.744
4gts 7TPGeranylgeranyl transferase type-2 subunit beta 2.5.1.60 0.699
4gtv 7TRGeranylgeranyl transferase type-2 subunit beta 2.5.1.60 0.680
1f5n GNPGuanylate-binding protein 1 / 0.660
1gx1 CDP2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase 4.6.1.12 0.660
1ky2 GNPGTP-binding protein YPT7 / 0.660
1svw GTPProbable GTP-binding protein EngB / 0.660
1wdt GTPElongation factor G (EF-G-2) / 0.660
2oap ANPType II secretion system protein (GspE-2) / 0.660
2xtn GTPGTPase IMAP family member 2 / 0.660
2z7q ACPRibosomal protein S6 kinase alpha-1 2.7.11.1 0.660
3ftq GNPSeptin-2 / 0.660
3tjz GNPADP-ribosylation factor 1 / 0.660
4goj GNPADP-ribosylation factor-like protein 3 / 0.660
4hdq GNPRas-related protein Rap-1b / 0.660
4hut ATPCob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 0.660
5cyp GSPSeptin-9 / 0.660