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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
4oav ACP 2-5A-dependent ribonuclease 3.1.26

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4oav ACP2-5A-dependent ribonuclease 3.1.26 1.153
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.866
4ceg ADPAurora kinase A 2.7.11.1 0.863
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.849
5dn3 ATPAurora kinase A 2.7.11.1 0.846
1mq4 ADPAurora kinase A 2.7.11.1 0.844
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.843
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.834
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.830
4utd ACPAurora kinase A 2.7.11.1 0.830
4dee ADPAurora kinase A 2.7.11.1 0.829
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.823
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.813
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.809
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.801
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.800
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.796
3c50 ADPRhodopsin kinase / 0.796
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.791
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.791
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.790
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.789
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.787
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.784
5dnr ATPAurora kinase A 2.7.11.1 0.781
3t8o ATPRhodopsin kinase / 0.780
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.778
5drd ATPAurora kinase A 2.7.11.1 0.778
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.776
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.776
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.775
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.774
4ysj ADPCalmodulin-like domain protein kinase / 0.773
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.771
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.771
5dt3 ATPAurora kinase A 2.7.11.1 0.769
2pui ADPMethylthioribose kinase 2.7.1.100 0.766
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.766
3c4z ADPRhodopsin kinase / 0.765
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.765
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.762
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.762
5ce3 ADPProtein kinase YopO / 0.757
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.756
4k33 ACPFibroblast growth factor receptor 3 2.7.10.1 0.756
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.755
2pyw ADPMethylthioribose kinase 2.7.1.100 0.754
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.754
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.751
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.749
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.748
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.747
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.747
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.746
4o1p ANPRibonuclease L / 0.746
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.742
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.742
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.742
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.742
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.742
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.741
5dt4 ATPAurora kinase A 2.7.11.1 0.740
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.739
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.739
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.739
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.736
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.736
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.735
5dos ATPAurora kinase A 2.7.11.1 0.734
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.733
4qny ANPMitogen activated protein kinase, putative / 0.733
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.732
2dwb ANPAurora kinase A 2.7.11.1 0.732
2olc ADPMethylthioribose kinase 2.7.1.100 0.732
2pul ACPMethylthioribose kinase 2.7.1.100 0.731
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.731
3cly ACPFibroblast growth factor receptor 2 / 0.730
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.728
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.728
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.727
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.726
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.726
5dr2 ATPAurora kinase A 2.7.11.1 0.726
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.724
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.724
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.723
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.723
4ork GDPBifunctional AAC/APH 2.3.1 0.722
4bn1 ADPAurora kinase A 2.7.11.1 0.720
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.719
3qc9 ADPRhodopsin kinase / 0.719
2pup ADPMethylthioribose kinase 2.7.1.100 0.718
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.718
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.717
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.717
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.715
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.714
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.714
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.713
4fu0 ADPD-alanine--D-alanine ligase / 0.713
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.712
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.712
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.712
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.711
4btj ATPTau-tubulin kinase 1 2.7.11.1 0.711
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.710
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.709
4xlv ACPInsulin receptor 2.7.10.1 0.709
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.708
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.708
4ffm ADPUncharacterized protein / 0.708
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.707
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.707
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.704
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.704
3nie ANPMitogen-activated protein kinase / 0.704
3c4x ATPRhodopsin kinase / 0.703
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.699
3a7j ADPSerine/threonine-protein kinase 24 2.7.11.1 0.699
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.697
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.697
1m0w ANPGlutathione synthetase 6.3.2.3 0.696
5dmz ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.696
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.694
4ic7 ANPMitogen-activated protein kinase 7 2.7.11.24 0.692
1cm8 ANPMitogen-activated protein kinase 12 / 0.691
2qoq ANPEphrin type-A receptor 3 2.7.10.1 0.691
3wo0 ADPAlanine--anticapsin ligase / 0.691
5iqf GDPBifunctional AAC/APH 2.3.1 0.691
4o4d ATPKinase / 0.690
1ol6 ATPAurora kinase A 2.7.11.1 0.689
3orm AGSSerine/threonine protein kinase / 0.689
2pml ANPUncharacterized protein / 0.688
4dh3 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.687
2p0a ANPSynapsin-3 / 0.685
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.685
4y0x ADPSerine/threonine-protein kinase PknG 2.7.11.1 0.685
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.684
3bu5 ATPInsulin receptor 2.7.10.1 0.682
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.681
4gyi ADPUncharacterized protein / 0.681
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.680
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.680
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.680
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.679
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.679
3myk ANPMyosin-2 heavy chain / 0.677
3tdv GDPGentamicin resistance protein / 0.677
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.676
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.675
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.674
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.673
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.672
2pun ACPMethylthioribose kinase 2.7.1.100 0.672
3tdw GDPGentamicin resistance protein / 0.672
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.671
5iqe GNPBifunctional AAC/APH 2.3.1 0.671
4ffr ATPUncharacterized protein / 0.670
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.669
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.669
4o0u ADNAurora kinase A 2.7.11.1 0.669
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.668
1xr1 ANPSerine/threonine-protein kinase pim-1 2.7.11.1 0.668
1ol7 ADPAurora kinase A 2.7.11.1 0.667
2fsn ADPArchaeal actin homolog / 0.667
2itn ANPEpidermal growth factor receptor 2.7.10.1 0.667
2pvr ANPCasein kinase II subunit alpha 2.7.11.1 0.667
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.667
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.667
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.667
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.667
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.666
4ffl ADPUncharacterized protein / 0.666
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.665
2qo9 ANPEphrin type-A receptor 3 2.7.10.1 0.665
4mv8 ACPBiotin carboxylase 6.3.4.14 0.665
2acx ANPG protein-coupled receptor kinase 6 2.7.11.16 0.664
2j0l ANPFocal adhesion kinase 1 2.7.10.2 0.664
4ifc ADPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.664
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.663
4o0w ADNAurora kinase A 2.7.11.1 0.663
5ckw ANPUncharacterized protein / 0.663
2dek SAHDiphthine synthase / 0.662
2ejj SAHDiphthine synthase / 0.662
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.662
2p6i SAHDiphthine synthase / 0.662
1rfu ADPPyridoxal kinase 2.7.1.35 0.661
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.661
2e8q SAHDiphthine synthase / 0.661
2eni SAHDiphthine synthase / 0.661
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.661
2owu SAHDiphthine synthase / 0.660
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.660
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.660
5eg3 ACPFibroblast growth factor receptor 2 / 0.660
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.659
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.659
1ol5 ADPAurora kinase A 2.7.11.1 0.658
2dxw SAHDiphthine synthase / 0.658
2e07 SAHDiphthine synthase / 0.658
2wtk ANPSTE20-related kinase adapter protein alpha / 0.658
4ix5 ANPUncharacterized protein / 0.658
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.658
2bme GNPRas-related protein Rab-4A / 0.657
2owf SAHDiphthine synthase / 0.657
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.657
5iqb GNPBifunctional AAC/APH 2.3.1 0.657
3oij SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.656
4n57 ADPAPH(2'')-Id / 0.656
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.655
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.655
2py3 ACPFibroblast growth factor receptor 2 / 0.654
3a8w ATPProtein kinase C iota type 2.7.11.13 0.654
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.653
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.653
3bc1 GNPRas-related protein Rab-27A / 0.653
3dqw AGSProto-oncogene tyrosine-protein kinase Src 2.7.10.2 0.653
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.652
3mia ANPCyclin-dependent kinase 9 2.7.11.22 0.652
4yhj AN2G protein-coupled receptor kinase 4 2.7.11.16 0.652
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
3c4w ATPRhodopsin kinase / 0.651
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
5iqg GDPBifunctional AAC/APH 2.3.1 0.651
3hgm ATPTRAP-T-associated universal stress protein TeaD / 0.650
3hko ANPCalcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands / 0.650
4crs AGSSerine/threonine-protein kinase N2 2.7.11.13 0.650