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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
1vhz APR ADP compounds hydrolase NudE 3.6.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1vhz APRADP compounds hydrolase NudE 3.6.1 0.809
1g7u PEP2-dehydro-3-deoxyphosphooctonate aldolase 2.5.1.55 0.744
4e5i 0N9Polymerase acidic protein / 0.744
3ung ADPCRISPR system Cmr subunit Cmr2 / 0.723
2itx ANPEpidermal growth factor receptor 2.7.10.1 0.691
4ajg F07cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A 3.1.4.17 0.682
1pag FMPAntiviral protein I 3.2.2.22 0.669
5k2b ZMAAdenosine receptor A2a / 0.669
2fb3 5ADGTP 3',8-cyclase 4.1.99.18 0.668
5uvi ZMAAdenosine receptor A2a / 0.667
5k2a ZMAAdenosine receptor A2a / 0.666
2eg2 ATPNitrogen regulatory protein P-II / 0.665
5iu8 6DZAdenosine receptor A2a / 0.665
3qfv NM7Serine/threonine-protein kinase MRCK beta 2.7.11.1 0.663
3b2t M33Fibroblast growth factor receptor 2 / 0.662
4q9e XXHPeptidoglycan recognition protein 1 / 0.662
2itv ANPEpidermal growth factor receptor 2.7.10.1 0.660
3dyl IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A / 0.660
4e5f 0N7Polymerase acidic protein / 0.660
5hq8 SAHHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.660
2x1l ADNMethionine--tRNA ligase / 0.658
1m67 BOAGlycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal 1.1.1.8 0.656
3ml2 SU0Carbonic anhydrase 2 4.2.1.1 0.656
4kw5 1W6Decaprenylphosphoryl-beta-D-ribose oxidase / 0.656
2vtl LZ5Cyclin-dependent kinase 2 2.7.11.22 0.655
1rag CTPAspartate carbamoyltransferase regulatory chain / 0.654
1zkn IBMcAMP-specific 3',5'-cyclic phosphodiesterase 4D 3.1.4.53 0.654
2ok7 A2PFerredoxin--NADP reductase, apicoplast / 0.654
2xf0 4UBSerine/threonine-protein kinase Chk1 2.7.11.1 0.654
1okm SABCarbonic anhydrase 2 4.2.1.1 0.653
2weh FB1Carbonic anhydrase 2 4.2.1.1 0.653
2zfi ADPKinesin-like protein KIF1A / 0.653
2a3b CFFEndochitinase B1 3.2.1.14 0.652
3k4y IPEIsopentenyl phosphate kinase 2.7.4.26 0.652
4dpg APCLysine--tRNA ligase 6.1.1.6 0.651
4ito MPXCarbonic anhydrase 2 4.2.1.1 0.651
4jia 1K3Tyrosine-protein kinase JAK2 / 0.651
1ho5 ADNProtein UshA 3.1.3.5 0.650
3nb5 R21Carbonic anhydrase 2 4.2.1.1 0.650
3v2j AZMCarbonic anhydrase 2 4.2.1.1 0.650
4kfb 1QPGag-Pol polyprotein 2.7.7.49 0.650