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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/1.000
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.478
4dpwAGSMevalonate diphosphate decarboxylase/0.464
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.462
4s1b2BALmo1466 protein/0.456
4r20AERCytochrome P450 family 17 polypeptide 2/0.455
2po7CHDFerrochelatase, mitochondrial4.99.1.10.454
3zkpERBErythromycin C-12 hydroxylase1.14.13.1540.454
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.453
4ktl1CQCytochrome P450/0.453
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.451
2qnqQN3Gag-Pol polyprotein3.4.23.160.450
1u3cFADCryptochrome-1/0.448
1k6vXN2Gag-Pol polyprotein3.4.23.160.447
1pkfEPDEpothilone C/D epoxidase1.140.446
1k6cMK1Gag-Pol polyprotein3.4.23.160.445
3bgcLJHGag-Pol polyprotein3.4.23.160.445
3pwhZMAAdenosine receptor A2a/0.442
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
2ejvNADL-threonine 3-dehydrogenase/0.440
4ktf1TMCytochrome P450/0.440