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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
3eth ATP N5-carboxyaminoimidazole ribonucleotide synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 1.153
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.902
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.805
1m0w ANPGlutathione synthetase 6.3.2.3 0.802
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.797
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.780
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.774
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.771
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.768
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.766
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.766
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.759
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.755
1pk8 ATPSynapsin-1 / 0.753
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.750
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.744
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.734
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.733
2pz5 ACPFibroblast growth factor receptor 2 / 0.730
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.729
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.729
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.728
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.725
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.724
5c1p ADPD-alanine--D-alanine ligase / 0.722
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.721
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.720
4fu0 ADPD-alanine--D-alanine ligase / 0.720
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.719
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.715
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.714
2zdg ADPD-alanine--D-alanine ligase / 0.713
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.712
4o4d ATPKinase / 0.711
4zgn ATPCell division cycle protein 123 / 0.710
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.708
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.706
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.704
3wnz ADPAlanine--anticapsin ligase / 0.704
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.704
1mq4 ADPAurora kinase A 2.7.11.1 0.703
4dee ADPAurora kinase A 2.7.11.1 0.702
2p0a ANPSynapsin-3 / 0.701
4ffm ADPUncharacterized protein / 0.701
4jrn ANPRhoptry kinase family protein / 0.698
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.696
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.692
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.692
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.691
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.690
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.690
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.689
2i8c ADPD-alanine--D-alanine ligase / 0.689
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.689
1px2 ATPSynapsin-1 / 0.684
3wo0 ADPAlanine--anticapsin ligase / 0.684
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.684
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.684
2pul ACPMethylthioribose kinase 2.7.1.100 0.683
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.682
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.682
4ceg ADPAurora kinase A 2.7.11.1 0.682
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.681
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.681
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.680
3ori AGSSerine/threonine protein kinase / 0.679
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.679
1bxr ANPCarbamoyl-phosphate synthase large chain / 0.678
2pui ADPMethylthioribose kinase 2.7.1.100 0.678
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.676
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.676
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.676
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.676
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.674
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
3bu5 ATPInsulin receptor 2.7.10.1 0.672
3t54 ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.671
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.671
4ffr ATPUncharacterized protein / 0.671
2j0l ANPFocal adhesion kinase 1 2.7.10.2 0.669
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.669
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.669
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.669
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.668
4bn1 ADPAurora kinase A 2.7.11.1 0.668
2j9g ADPBiotin carboxylase 6.3.4.14 0.667
3ies M24Luciferin 4-monooxygenase 1.13.12.7 0.667
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.666
2py3 ACPFibroblast growth factor receptor 2 / 0.665
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.665
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.664
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.664
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.664
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.664
2olc ADPMethylthioribose kinase 2.7.1.100 0.662
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.662
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.662
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.661
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.661
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.661
5dr2 ATPAurora kinase A 2.7.11.1 0.661
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.660
5iqh GNPBifunctional AAC/APH 2.3.1 0.660
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.659
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.658
2bku GTPGTP-binding nuclear protein Ran / 0.657
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.657
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.656
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.656
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.656
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.656
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.656
4qml ANPSerine/threonine-protein kinase 24 2.7.11.1 0.656
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.656
5dt3 ATPAurora kinase A 2.7.11.1 0.656
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.655
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.654
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.653
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.653
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.653
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.652
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.652
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.651
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.651
3cly ACPFibroblast growth factor receptor 2 / 0.651
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.650
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.650