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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
2ioa ADP Bifunctional glutathionylspermidine synthetase/amidase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 1.239
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 1.061
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 1.042
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.921
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.895
3wo0 ADPAlanine--anticapsin ligase / 0.874
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.856
3wnz ADPAlanine--anticapsin ligase / 0.844
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.842
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.836
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.833
5c1o ANPD-alanine--D-alanine ligase / 0.829
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.827
2p0a ANPSynapsin-3 / 0.811
2hgs ADPGlutathione synthetase 6.3.2.3 0.810
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.804
3tw6 ADPPyruvate carboxylase / 0.781
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.780
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.774
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.769
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.768
4ysj ADPCalmodulin-like domain protein kinase / 0.764
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.761
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.759
3wo1 ADPAlanine--anticapsin ligase / 0.758
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.757
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.755
4ffl ADPUncharacterized protein / 0.754
5c1p ADPD-alanine--D-alanine ligase / 0.751
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.746
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.745
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.744
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.744
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.738
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.738
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.736
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.735
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.735
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.732
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.726
5ce3 ADPProtein kinase YopO / 0.725
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.724
3pff ADPATP-citrate synthase 2.3.3.8 0.723
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.723
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.723
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.722
4ffm ADPUncharacterized protein / 0.720
4xlv ACPInsulin receptor 2.7.10.1 0.720
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.717
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.717
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.716
4ceg ADPAurora kinase A 2.7.11.1 0.716
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.716
3rv4 ADPBiotin carboxylase 6.3.4.14 0.715
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.714
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.712
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.711
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.710
4ffr ATPUncharacterized protein / 0.710
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.709
2xuu ADPDeath-associated protein kinase 1 2.7.11.1 0.708
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.708
2vqd AP2Biotin carboxylase 6.3.4.14 0.707
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.707
5bpf ADPD-alanine--D-alanine ligase / 0.707
3bu5 ATPInsulin receptor 2.7.10.1 0.706
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.704
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.702
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.701
4crs AGSSerine/threonine-protein kinase N2 2.7.11.13 0.701
2x0q ATPAlcaligin biosynthesis protein / 0.700
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.700
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.699
2zdg ADPD-alanine--D-alanine ligase / 0.697
1mq4 ADPAurora kinase A 2.7.11.1 0.696
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.696
1m0w ANPGlutathione synthetase 6.3.2.3 0.695
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.694
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.691
2ydo ADNAdenosine receptor A2a / 0.691
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.690
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.688
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.688
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.688
1pkg ADPMast/stem cell growth factor receptor Kit 2.7.10.1 0.686
4cng SAHSpoU rRNA methylase / 0.686
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.685
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.684
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.684
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.681
4i0b CMPcAMP-activated global transcriptional regulator CRP / 0.681
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.681
2a19 ANPInterferon-induced, double-stranded RNA-activated protein kinase 2.7.11.1 0.680
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.680
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.679
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.679
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.679
2fyc GDUBeta-1,4-galactosyltransferase 1 2.4.1 0.678
3ab8 ATPUncharacterized protein / 0.678
3hyo ADPPyridoxal kinase / 0.678
4dee ADPAurora kinase A 2.7.11.1 0.678
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.678
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.677
4nm0 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.677
1u54 ACPActivated CDC42 kinase 1 / 0.676
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.676
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.676
1cgp CMPcAMP-activated global transcriptional regulator CRP / 0.675
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.675
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
3ryp CMPcAMP-activated global transcriptional regulator CRP / 0.674
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.674
4jlb ADPAdenylate kinase / 0.674
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.674
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.673
2qmm SAMtRNA (pseudouridine(54)-N(1))-methyltransferase / 0.672
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.672
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.672
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.671
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.671
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.671
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.670
2pml ANPUncharacterized protein / 0.670
2wq7 FADRE11660p / 0.670
3cvu FADRE11660p / 0.670
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.670
5cb4 ACPTubulin tyrosine ligase / 0.670
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.669
4q5h ANPProtein kinase OspG 2.7 0.669
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.669
5g53 NECAdenosine receptor A2a / 0.669
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.668
1px2 ATPSynapsin-1 / 0.668
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.668
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.668
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.668
3mj4 URMUDP-galactopyranose mutase / 0.667
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.666
2dv7 SAHDiphthine synthase / 0.666
3mhy ATPNitrogen regulatory protein P-II 1 / 0.666
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.666
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.666
2cvu CDPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.665
3c50 ADPRhodopsin kinase / 0.665
4jlp ADPAdenylate kinase / 0.665
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.665
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.665
4xd1 T3QQdtf / 0.665
2huv SAHDiphthine synthase / 0.664
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.664
1p52 ADPArginine kinase 2.7.3.3 0.663
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.663
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.662
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.662
4xbo SAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ 2.1.1.200 0.662
1qrt ATPGlutamine--tRNA ligase 6.1.1.18 0.661
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.661
3hpr AP5Adenylate kinase / 0.660
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.660
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.660
4zol ACPTubulin tyrosine ligase / 0.660
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.658
2cx8 SAHRibosomal RNA small subunit methyltransferase E / 0.657
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
4l2i FADElectron transfer flavoprotein alpha/beta-subunit / 0.657
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.656
2pb6 SAHDiphthine synthase / 0.656
3oij SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.656
4e1b TXAThreonylcarbamoyl-AMP synthase 2.7.7.87 0.656
4i0a CMPcAMP-activated global transcriptional regulator CRP / 0.656
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.656
5dmz ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.656
2pca SAHDiphthine synthase / 0.655
3cr3 ADPPTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL 2.7 0.655
4ehy ADPTetraacyldisaccharide 4'-kinase / 0.655
5c93 ACPTwo-component system histidine protein kinase / 0.655
1foa UD1Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase 2.4.1.101 0.654
1vce SAHDiphthine synthase / 0.654
3g8c ADPBiotin carboxylase 6.3.4.14 0.654
3ibq ATPPyridoxal kinase / 0.654
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.654
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.653
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.653
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.653
4r8h SP1cAMP-activated global transcriptional regulator CRP / 0.653
2eh2 SAHDiphthine synthase / 0.652
2owv SAHDiphthine synthase / 0.652
2q0g UPUPoly(A) polymerase, putative / 0.652
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.652
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.652
4bn1 ADPAurora kinase A 2.7.11.1 0.652
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.652
1v3s ATPSignaling protein / 0.651
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.651
1s4d SAHUroporphyrinogen-III C-methyltransferase 2.1.1.107 0.650
2dsh SAHDiphthine synthase / 0.650
2dsi SAHDiphthine synthase / 0.650