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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
3k5h ATP Phosphoribosyl-aminoimidazole carboxylase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 1.149
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.902
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.792
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.787
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.785
1pk8 ATPSynapsin-1 / 0.781
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.779
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.766
2p0a ANPSynapsin-3 / 0.763
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.762
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.762
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.761
1m0w ANPGlutathione synthetase 6.3.2.3 0.759
4fu0 ADPD-alanine--D-alanine ligase / 0.755
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.754
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.752
4ffr ATPUncharacterized protein / 0.750
5c1p ADPD-alanine--D-alanine ligase / 0.750
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.745
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.743
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.738
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.738
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.738
1px2 ATPSynapsin-1 / 0.736
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.733
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.731
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.729
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.728
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.727
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.727
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.727
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.726
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.726
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.725
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.723
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.721
4o1p ANPRibonuclease L / 0.721
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.720
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.719
2zdg ADPD-alanine--D-alanine ligase / 0.719
3rv4 ADPBiotin carboxylase 6.3.4.14 0.718
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.717
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.717
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.715
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.714
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.713
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.713
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.712
4ffl ADPUncharacterized protein / 0.712
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.711
4zgn ATPCell division cycle protein 123 / 0.710
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.709
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.709
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.709
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.708
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.707
3wo0 ADPAlanine--anticapsin ligase / 0.707
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.706
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.705
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.704
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.703
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.702
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.702
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.701
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.701
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.700
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.697
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.697
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.693
3lmh ADPMyosin heavy chain kinase A 2.7.11.7 0.693
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.693
4ceg ADPAurora kinase A 2.7.11.1 0.692
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.691
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.690
1mq4 ADPAurora kinase A 2.7.11.1 0.690
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.690
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.689
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.688
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.687
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.686
1z6t ADPApoptotic protease-activating factor 1 / 0.686
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.686
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.685
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.685
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.684
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.683
4jqe ANPCasein kinase II subunit alpha 2.7.11.1 0.683
3bu5 ATPInsulin receptor 2.7.10.1 0.682
3wo1 ADPAlanine--anticapsin ligase / 0.682
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.682
5dos ATPAurora kinase A 2.7.11.1 0.682
3lla ACPMyosin heavy chain kinase A 2.7.11.7 0.681
3wnz ADPAlanine--anticapsin ligase / 0.681
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.681
5dt4 ATPAurora kinase A 2.7.11.1 0.681
2pz5 ACPFibroblast growth factor receptor 2 / 0.679
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.677
1cm8 ANPMitogen-activated protein kinase 12 / 0.676
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.676
2pui ADPMethylthioribose kinase 2.7.1.100 0.676
4qny ANPMitogen activated protein kinase, putative / 0.676
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.675
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.675
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.674
4utd ACPAurora kinase A 2.7.11.1 0.674
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.673
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.673
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.672
5iqa GNPBifunctional AAC/APH 2.3.1 0.672
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.670
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.670
4ffm ADPUncharacterized protein / 0.670
2j9g ADPBiotin carboxylase 6.3.4.14 0.669
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.669
5dr2 ATPAurora kinase A 2.7.11.1 0.669
2hgs ADPGlutathione synthetase 6.3.2.3 0.668
3g8d ADPBiotin carboxylase 6.3.4.14 0.667
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.667
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.666
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.666
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.666
2j0l ANPFocal adhesion kinase 1 2.7.10.2 0.666
2qen ADPWalker-Type ATPase / 0.666
4g36 SLULuciferin 4-monooxygenase 1.13.12.7 0.666
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.666
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.665
3t8o ATPRhodopsin kinase / 0.665
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.665
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.664
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
1h8h ADPATP synthase subunit alpha, mitochondrial / 0.664
1h8h ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.664
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.664
2py3 ACPFibroblast growth factor receptor 2 / 0.663
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.663
5eg3 ACPFibroblast growth factor receptor 2 / 0.663
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.661
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.661
4bw9 ANPPyrrolysine--tRNA ligase / 0.661
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.661
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.660
5dnr ATPAurora kinase A 2.7.11.1 0.660
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.659
5ifi PRXAcetyl-coenzyme A synthetase / 0.659
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.658
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.658
3dqw AGSProto-oncogene tyrosine-protein kinase Src 2.7.10.2 0.657
3mia ANPCyclin-dependent kinase 9 2.7.11.22 0.657
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.656
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.656
4ifc ADPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.656
5byl GCPBifunctional AAC/APH 2.3.1 0.656
2p2b PRXAcetyl-coenzyme A synthetase / 0.655
2p2m PRXAcetyl-coenzyme A synthetase / 0.655
5iqi GNPBifunctional AAC/APH 2.3.1 0.655
2olc ADPMethylthioribose kinase 2.7.1.100 0.654
4bn1 ADPAurora kinase A 2.7.11.1 0.654
4dee ADPAurora kinase A 2.7.11.1 0.654
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.653
2ijm ADPFocal adhesion kinase 1 2.7.10.2 0.653
4mv8 ACPBiotin carboxylase 6.3.4.14 0.653
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.652
3a8w ATPProtein kinase C iota type 2.7.11.13 0.652
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.652
4pfp ADPUnconventional myosin-VI / 0.652
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.652
2qmm SAMtRNA (pseudouridine(54)-N(1))-methyltransferase / 0.651
1gy3 ATPCyclin-dependent kinase 2 2.7.11.22 0.650
3cr3 ADPPTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL 2.7 0.650
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.650
4cng SAHSpoU rRNA methylase / 0.650