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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
5byl GCP Bifunctional AAC/APH 2.3.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5byl GCPBifunctional AAC/APH 2.3.1 1.070
5iqh GNPBifunctional AAC/APH 2.3.1 0.962
5iqb GNPBifunctional AAC/APH 2.3.1 0.917
5iqd GNPBifunctional AAC/APH 2.3.1 0.895
5iqi GNPBifunctional AAC/APH 2.3.1 0.888
5iqa GNPBifunctional AAC/APH 2.3.1 0.881
5iqe GNPBifunctional AAC/APH 2.3.1 0.868
5iqf GDPBifunctional AAC/APH 2.3.1 0.838
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.820
4ork GDPBifunctional AAC/APH 2.3.1 0.797
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.791
3tdw GDPGentamicin resistance protein / 0.786
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.775
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.771
3tdv GDPGentamicin resistance protein / 0.761
1m0w ANPGlutathione synthetase 6.3.2.3 0.750
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.749
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.746
2pz5 ACPFibroblast growth factor receptor 2 / 0.745
3cly ACPFibroblast growth factor receptor 2 / 0.745
4o4d ATPKinase / 0.744
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.740
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.728
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.728
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.727
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.726
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.724
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.720
3c50 ADPRhodopsin kinase / 0.716
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.715
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.713
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.712
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.711
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.710
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.709
4ceg ADPAurora kinase A 2.7.11.1 0.705
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.705
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.704
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.701
4n57 ADPAPH(2'')-Id / 0.700
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.698
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.698
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.698
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.697
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.696
2pup ADPMethylthioribose kinase 2.7.1.100 0.696
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.696
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.696
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.695
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.695
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.694
3c4z ADPRhodopsin kinase / 0.693
2pzp ACPFibroblast growth factor receptor 2 / 0.692
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.691
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.691
2pyw ADPMethylthioribose kinase 2.7.1.100 0.690
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.690
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.689
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.688
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.688
5iqg GDPBifunctional AAC/APH 2.3.1 0.687
2olc ADPMethylthioribose kinase 2.7.1.100 0.686
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.684
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.684
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.682
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.682
3t8o ATPRhodopsin kinase / 0.682
4gyi ADPUncharacterized protein / 0.682
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.682
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.682
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.681
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.680
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.679
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.678
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.677
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.677
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.677
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.676
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.675
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.675
4ysj ADPCalmodulin-like domain protein kinase / 0.675
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.674
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.673
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.672
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.672
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.671
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.671
2py3 ACPFibroblast growth factor receptor 2 / 0.670
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.669
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.669
2hgs ADPGlutathione synthetase 6.3.2.3 0.669
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.669
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.668
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.668
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.667
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.667
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.667
4ffr ATPUncharacterized protein / 0.667
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.667
3llt ANPProtein serine/threonine kinase-1 / 0.666
3wnz ADPAlanine--anticapsin ligase / 0.666
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.666
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.666
1mq4 ADPAurora kinase A 2.7.11.1 0.665
4xlv ACPInsulin receptor 2.7.10.1 0.665
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.664
5bsm ATP4-coumarate--CoA ligase 2 6.2.1.12 0.663
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.662
2dwb ANPAurora kinase A 2.7.11.1 0.661
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.661
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.661
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.661
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.660
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.660
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.660
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
4dee ADPAurora kinase A 2.7.11.1 0.660
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.660
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.659
1n2e APCPantothenate synthetase 6.3.2.1 0.659
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.659
3bu5 ATPInsulin receptor 2.7.10.1 0.659
3igo ANPCalmodulin-domain protein kinase 1, putative / 0.659
5cvf ATPCasein kinase II subunit alpha 2.7.11.1 0.659
2pul ACPMethylthioribose kinase 2.7.1.100 0.658
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.657
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.656
3c4w ATPRhodopsin kinase / 0.656
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.656
4utd ACPAurora kinase A 2.7.11.1 0.656
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.655
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
4jr7 GNPCasein kinase II subunit alpha 2.7.11.1 0.655
5drd ATPAurora kinase A 2.7.11.1 0.655
3qc9 ADPRhodopsin kinase / 0.653
5dr2 ATPAurora kinase A 2.7.11.1 0.653
1ss9 UPFLgtC / 0.652
2pun ACPMethylthioribose kinase 2.7.1.100 0.652
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.652
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.651
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.650
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.650
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.650